Destiny Book 1: Dark Vengeance

by SirScribe

Rating: teen
Tags: King Sombra, Queen Chrysalis, Adventure, Crossover, Main 6, Discord, My Little Pony: Friendship is Magic, Nightmare Moon
Length: 49947

The Mane 6 face their biggest challenge yet as they go horn-to-horn against their darkest foes.

King Sombra. Queen Chrysalis. Nightmare Moon. Discord. Alone, they failed in taking Equestria from the Princesses and the Mane 6. United, they become a threat beyond anything the girls have seen. With nothing more than a grudge against the Crown and the Elements, these 4 very different foes will rise up for the chance to reclaim what is theirs.

Join Twilight Sparkle as she journeys across Equestria with brand new friends to find the power necessary to rid the world of this impossible nightmare. This will be the biggest fight they've had yet. Takes place between season 3 and 4.

Published 2015-01-07 16:30:02 UTC
Last updated 2015-09-29 18:33:33 UTC

Enemies assemble

1 week before Twilight's coronation

Princess Celestia paced the throne room, continuously muttering under her breath. It was now sunset in Equestria, and as Celestia feared, Twilight had passed all of the tests she had given her. From Nightmare Moon to Sombra and the Crystal Empire, it seemed to the alicorn that there would be nothing to stop Twilight's rise.

That's what worried her.

Sitting at the throne was Princess Luna, who was found glaring at the journal in front of her. The writing inside was Starswirl the Bearded, but ever since Sombra's defeat, Luna had argued against what she had to do. She was told of what Starswirl had set out to do, yet the idea itself was madness. The circumstances surrounding the journal and Twilight's destiny was still too much to think about.

"Sister, please reconsider this--this madness! It is true that we must think about the future, but Twilight is young filly who still has much to learn! I beg you, Celestia, don't have her go through this," Luna pleaded.

Celestia stopped pacing the room. "You don't understand Luna. For a thousand years, I've given that test to all the students who had proven themselves, but none have managed to do so. I had to wait a thousand years so the timing could be perfect," she said.

"But the prophecy--"

"Luna, you and I both know what happens when somepony tries to run away from a prophecy. Most of the prophecy had already come to pass, just not in the right order."

"So I've heard. The rumor of the Gates?"

"Destroyed. I fear we will see many foes from Tartarus rise once more. Now is the time, Luna. Twilight is the one," Celestia argued. "You've seen her power!"

"The power of a filly looking to please her idol. You may not know, but she idolizes you more than any other, including Starswirl himself. If anything, she will be more dangerous with unlimited power that comes with alicorns. She needs more time."

Celestia sighed. "I fear we are out of time. I will have this journal delivered to her immediately. Have faith, sister," she said.

"I do have faith. This is why I worry. I shall continue to do as you have requested, sister. She must still not know?"

"Not yet. I know how eager you are to speak the truth, but this was a favor for me. Keep an eye on her please?"

Luna nodded. Celestia sighed as she walked out of the throne room. As the doors slammed shut as Luna looked out into the night sky. She sighed as she once remembered how much she wished for the night to be adored by everypony in the realm.

Those were darker days Luna, she thought to herself. But darker days are soon on the way.

7 months following Twilight's coronation

Thunder and lightning dominated the Canterlot night. With the storm passing over the Everfree Forest and parts of the desert, most ponies really had a reason to remain indoors for the night. The scheduled Galaxy Watch, the newest event hosted by Princess Luna, just had to wait until the storm passed. Little did everypony know that a bigger storm was headed their way. A storm unlike any before it. This storm had a cruel way of moving in, especially since the crowning of the newest princess: Twilight Sparkle.

Ever since her coronation, Twilight had taken every single royal job Princess Celestia threw at her. Being forced to travel across the planes of Equestria, Twilight had to say goodbye to her friends in Ponyville to familiarize herself with the land she was used to protecting. Days turned into weeks, and weeks turned into months. Soon, the Mane 6 began drifting off in separate directions. While this destroyed Twilight, she felt fear that something will happen and the Elements will be too far apart to work properly.

In the darkened alleyways of Canterlot, a group of individuals met. Judging by the sizes of their shadows, there were three equines present. Two alicorns and one unicorn with an oddly shaped horn. The three were conversing with themselves when a slithering shadow formed next to the unicorn. "Are we all here?"

One of the alicorns nodded. "All except for the blue one. She proclaimed that she wasn't going ahead with this operation. And she actually defeated Twilight Sparkle!"

The snake-like figure nodded its misformed head. "I expected that from a friend of hers. Anyway, as long as we all are here, we can begin."

The unicorn stepped forward. "Who put you in charge of this operation? Out of all of us, I am royalty! I am to be given the right to lead us!"

"Nay, the powers of this group must be ours! We will not serve under the leadership of a failed king!" One alicorn said.

"I am also royalty! I am a greater power than all of you. Plus, I have an army and hungry Changelings!" the other said.

"You should've been there the last Hearts and Hooves Day, I heard there was a love poison involved," Nightmare muttered.

The snake sighed. "I don't have to put up with this. I assembled you all back from your defeat in hopes that you will aid me in this. King Sombra, I was able to find your horn and bring you back from obliteration so don't forget that. Chrysalis, let's not forget that it was I who sought you out after you were defeated!"

Chrysalis growled. "I don't care. Besides, I would've been fine without your help."

Sombra laughed. "You were thrown out of Canterlot by the power of Love. The very substance that you feed on! You're pathetic!"

"Says the unicorn who was defeated by a crystal. I was defeated by real magic! And you, Nightmare, what's your story?"

The alicorn shuffled in her place. "The Elements of Harmony, but I was never truly defeated!"

The snake laughed. "You were cornered by 6 ponies who barely knew each other, tried to destroy the Elements, and just stood there while the Elements were taking their new form. If I was you, I would've put down Twilight before her Element was assembled. At least defeat somepony," the snake said. “Besides, I saved you just barely so keep that in mind!”

"Oh please Discord! You befriended the enemies. How do we know you are with us?" Nightmare Moon stated.

"Because I was the one who found all of you and assembled you. I have big plans for Equestria after what happened over a thousand years ago. My empire was taken from me!"

"Mine too!" Sombra declared.

"Mine as well!" Nightmare declared.

"And my children were reduced to scavengers thanks to Celestia!" Chrysalis said.

Discord sighed. "Then we all have an understanding. The enemy is Celestia. Our weapons: the Elements and their bearers. If I understand correctly, all 6 of them parted ways for the time being. You all have your targets, yes?"

All 3 of them nodded. "Then by tomorrow night, Equestria will be ours, and Celestia will be out of the way. We will finally have our revenge."

All 4 laughed maniacally. A crack of thunder and a lightning bolt revealed the four villains as they laughed. The darkness was rising again.

Twilight groaned as she stirred to consciousness. Sunlight broke through her suite in Canterlot as she rubbed her head. She raised her head off her pillow and looked around. That was hard with crusty eyes and an out of control mane. She blew the biggest clump of her mane out of her vision to see clearly. Still crusty eyes, but what are you going to do when you spent the last 3 weeks doing damage control.

Word of Twilight's journey into the human world grabbed a lot of attention in Equestria. Ponies declared that the royal family had the power to cross dimensions and bring deadly creatures to their world. After a while, Cadence had to publicly report that the mirror disappeared. That calmed some tension in Equestria, but ponies were still outraged that such a secret was being kept from them. Ever since then, Twilight has had letters coming in, both good and bad. Some ponies called her brave while others claimed she was a traitor to her own kind.

She dusted all the letters from her bed and walked over to her mirror. She had bags under her eyes. Something nopony liked seeing. She used her magic to calm her mane, but it was still wild. At least it was a bit presentable. She extended her wings to get another look at them. Ever since she was torn away from Ponyville, she kept thinking that her ordeal in the human world and her wings were just a dream. She always imagined waking up in her library without wings and everything back to normal.

She never got that fantasy.

She sighed. "Another day of training Twi. Another day with Celestia."

Suddenly, she heard a burp originate from behind her. She turned. Turns out to be only Spike, who was half buried in letters he helped read the previous night. Next to him was a scroll wrapped in a gray ribbon. Princess Celestia probably, she thought.

She levitated the scroll to her and began to read. She had to reread the letter. It read:

Dear Twilight Sparkle,

I'm afraid I will have to cancel our lessons for today. An emergency has arisen in Manehattan and I must be there to reassure the citizens that all is well. Meanwhile, I left Princess Luna in charge of the castle. Since you have shown a great improvement in your studies, myself and Princess Luna have agreed to allow you the whole day off. Go on and enjoy life beyond the castle AND library. The storm really brought out the beauty of Equestria.

Enjoy,

-Princess Celestia

Twilight smiled. She heard Spike groan from pain. "Who was it from?" he asked in his sleep.

"Princess Celestia. Something is happening in Manehattan and she left to take care of it. Why didn't she take Luna with her?" Twilight asked.

"Maybe Princess Luna was too tired of guarding the night," he said.

Twilight nodded. "Maybe you're right. Besides, today we have a day off. Wanna head out somewhere?"

Spike sat up. "How about we go visit our friends? It's been a while since we've seen the girls."

Twilight chuckled. "You just want to see Rarity, don't you?"

Spike blushed. "You make it sound like I don't miss our friends."

Twilight raised an eyebrow. "Do you miss our friends?"

"Of course, but I miss Rarity more."

Twilight laughed, and left to go wash up. She entered her wash room and immediately stared at the mirror. This is the face of a Princess, she thought to herself. I look hideous!

The lavender princess splashed water over her face before making her way to the shower. The warm water soothed Twilight as she allowed the heat to relax her already aching muscles. She had either been on her hooves most of the day or sitting down and responding to angry letters from ponies she didn't know.

As the water trickled down her back, Twilight's mind immediately went to the magic mirror in the Crystal Empire, and of course, her friends on the other side. They promised to help Sunset Shimmer with the transition, but even she was worried about her. She wasn't exactly kind to the students at Canterlot High. Some would probably enact revenge.

Twilight shook out of her train of thought. She shut off the shower and brushed her mane. She returned to her room to see Spike clearing his throat, probably so his voice would sound deeper for Rarity. Twilight rolled her eyes and laughed as she scooped Spike up. Together, they made their way to the outside of the castle where they would later fly off.

Meanwhile, the scroll that Twilight read suddenly grew a face. Discord had black ink written all over his face as he chuckled. "Phase 1 is a go," he muttered as he disappeared from the room.

Return to Ponyville

Twilight hated flying in the morning.

The recent storm left most of Canterlot in a heavy fog. The pegasus ponies were quick to conjure up such a storm for the area, but there were talks among the unicorns of Canterlot: the storm wasn't supervised by the pegasi. Twilight immediately dismissed such an accusation. It was impossible for a storm to exist without the pegasi. Her beliefs, however, were challenged in the human world.

Speaking of the human world, Twilight grew anxious since she returned. Why? To return to that world and learn more about it. She was hoping her friends on the other side were helping Sunset Shimmer in the transition from aspiring ruler of two dimensions to a regular teenager with the hope of graduating without anything going wrong.

A strong gust of wind rocked Twilight over the fields of Ponyville. With Spike on her back, Twilight tried to stabilize herself. "It's a bit cold up here, ya know?" Spike asked.

Twilight nodded. "The pegasi really did a good job with the storm last night. It reminds me of the storm that we had in Ponyville a few years ago," she said.

"The one I missed?"

Twilight nodded. "Also the night Applejack and Rarity slept over."

Spike facepalmed. Twilight chuckled. She never told Spike that Rarity was at their place the one night he wasn't. "Of all the days..."

Twilight burst into laughter. After a few more minutes, Ponyville was in sight. It was pretty foggy, much like the scene of a zombie movie. Or a novel. While they were fiction, Twilight enjoyed reading about what might happen if a zombie outbreak ever happened. She read a series of books from many great authors, although one author actually put himself as the leader of a group in one of the books. Twilight found that book intriguing and hoped that a second would be released soon.

She caught sight of her library. It looked the same as before. She looked around. Ponies were beginning their usual routines of opening shops and selling produce. She didn't see Applejack's cart though. "I don't see Applejack," Spike said.

Twilight nodded. Ever since she moved back to Canterlot, her friends kind of drifted apart. Applejack left to travel to Appleloosa for business. To her, it was an excuse to get away from Ponyville. Twilight would sometimes get a letter from Applejack, but it was only a status report. She found a nice spot to land behind a bush and touched down without being seen. She would always be crowded by ponies in Canterlot, but that was for advice. She was the princess who didn't spend time in the throne room. She had no idea what she was in for the moment she landed in Ponyville. Her hooves touched the earth, and she sighed. It was good to be back.

Spike jumped off her back, and that's when it all happened. The dragon burped, sending green flames into the sky. The scroll had appeared. Twilight levitated it towards her, but before she could read it, she heard commotion from behind the bushes. From behind the bushes, a crowd of ponies ran toward her.

“It’s the princess!” one stallion exclaimed.

"Spike, RUN!"

Spike jumped on Twilight's back, and she ran. Stallions had roses in their mouths. This motivated Twilight to run even faster. She saw the library in front of her. If she could get in, then she would be safe. She was about to perform an Unlocking Spell on the door, but it swung open. Inside was Pinkie Pie. "Twilight! Hurry up!"

She looked back at the crowd. They were getting closer. She poured her magic into her Teleportation Spell, and teleported to the doormat of her old home. She ran in, and shut the door behind her. Pinkie smiled as she turned the lights on. "TWILIGHT! GOOD TO SEE YOU AGAIN!"

Twilight collapsed. "Pinkie?! What the hay is going-?"

Pinkie shoved her hoof into Twilight's mouth. "They could be listening. Shhhhh."

Twilight rolled her eyes and used her magic to expunge the hoof from her mouth. "You were yelling a moment ago. What's going on?"

Pinkie smiled. "Well, nopony is still used to being in the same town as a princess. Ever since your coronation, everypony just wants to remember that they played host to a princess."

"Then explain the roses!"

Pinkie laughed. "Some want to remember more."

Twilight groaned. First was the whole controversy surrounding her and the new guard of the Crystal Empire, now it's this. This just proves that labels really do change things for you. "I guess you finally had time to yourself today, huh?" Pinkie asked.

Twilight nodded. "Princess Celestia sent me a letter saying there was trouble in Manehattan and she was tending to the matter. Strange thing is, all the guards were at their posts as I was leaving Canterlot," she said.

"Maybe they are the fallback. You never know, something could happen."

"Good point Pinkie."

Twilight looked around at her library. Except for the fact that all the books were dusty, everything was the same. The scorch mark on the floor when she was teleported, the stallion bust in the middle of the room, and the glass case that held the Elements of Harmony was undisturbed. Spike left to check the kitchen while Twilight picked a book from the shelves and began to read.

Pinkie paced around the library. She occasionally picked a book, flipped through the book, and dropped it on the floor. This alarmed Twilight. Pinkie was never this inconsiderate with her library. She never threw books on the ground without care. Pinkie stopped at a few books and put them on the center table, but that was all she did. "Hey Twilight, I've been wondering."

"About?"

She pointed at the glass case. "Can anypony lift that case?"

Twilight raised an eyebrow. What a weird question. "Just myself and the princesses. Why do you ask?"

She shrugged. "I was just wondering. I spotted some ponies wandering too close to the library several times while you were away. I was wondering if stealing the Elements was even possible."

A burp erupted from the kitchen. Twilight rolled her eyes. "Spike, you know some of that food is old, right?"

"Twilight, I'm not eating. It's another letter from the princess," Spike called out.

Twilight stood and walked over to the kitchen. Spike held up the letter, which had a black ribbon tied around it. Twilight had never seen a black ribbon letter before. She unraveled it and began to read. Immediately she felt chills running down her spine.

Twilight!

Listen to me very carefully. Disregard the letter from me earlier. I never sent you a letter about Manehattan. You need to secure the Elements immediately! You are in terrible danger. Do not react to this letter in any way around anypony. Nopony must know that something has happened. I've alerted the guards. Be ready to evacuate Ponyville. Oh dear Me, they found me. Be careful Twili

The letter stopped there. It was in Celestia's writing, she was sure of that. It appeared to have been rushed. Her name was dragged out in black ink. On the top corner, a large blot of ink stained the paper.

Suddenly, she heard a sigh from behind her. Twilight and Spike turned to see Pinkie behind them. "And we were so close." Her eyes glowed green.

Twilight gasped and took a fighting stance. She shielded Spike. "Spike, get out of here!"

Spike turned to run, but was suddenly hit with a green light. Twilight turned to see Spike sprawled across the floor. He was knocked out. Above him was two changelings with their magic auras charged up.

Twilight summoned a Stunning Spell from her arsenal of combat spells. Before she could fire, she was hit upside the head by something hard and metal. Her last moment of consciousness was three changelings standing proud above her. Behind them, Queen Chrysalis was grinning. "Looks like you left your guard down, Princess Twilight. How very unlike you."

Twilight tried to force a sentence to rebuttal, but fell prey to the pain and passed out. Once she did, the Elements disappeared behind the Changelings.

Train ride gone south

Ever since they got back from the Crystal Empire, Princess Celestia requested that Twilight move permanently to Canterlot so she man advance her studies on becoming a princess. Even though she learned a lot in her time in Ponyville, Twilight still had a lot to learn when it came to running a kingdom. Celestia's request ripped apart the Mane 6. Rainbow and Fluttershy returned to Cloudsdale, Rarity continued living in Ponyville along with Pinkie. Applejack, well, decided to travel.

Applejack traveled throughout Equestria in search for something to occupy her life since Twilight left. She traveled from Manehattan, where she visited her Aunt and Uncle Orange, to Appleloosa to catch up with some family. She missed spending time with her family, especially since the cutie mark dilemma a few weeks back.

The farm pony was at the station when she heard what was going on. Rumors began to circulate that Princess Twilight was in Ponyville. Applejack lit up. It had been a while since she had seen her friend, and since she was in Ponyville, it was a great time to catch up. She changed her ticket for one to Ponyville, and boarded the train. She was full of happiness. The gang was coming back together.

Unfortunately for Applejack, the train broke down half way through Ghastly Gorge. The farm pony groaned as the brakes were heavily applied. She didn’t dare stare out the window. Train delays were always something to get frustrated over. She looked around the train. Other ponies were confused and angry over the train delay.

Applejack was about to go to sleep when she heard something familiar. A voice that she grew sick of back in Ponyville. "You must let Trixie leave the train! Trixie demands it!"

"Sorry Trixie, but you can't! We are currently stuck in the middle of the Gorge. You must wait until we get to Ponyville before you can change trains," the conductor said.

“But it’ll be too late. I need to get off now!”

Applejack spun around. Sure enough, Trixie, the Great and Powerful pain in the plot, was in the back arguing with the conductor. Applejack rolled her eyes. Figures that Trixie would cause a commotion. Trixie spun around and immediately saw Applejack. Trixie walked past the conductor and sat next to Applejack. The farm pony lowered her hat just slightly. “What do ya want?" Applejack asked rather harshly.

Trixie's ears fell. "Look, can we look past what Trixie did in Ponyville?"

Applejack looked over at her. "No!"

Trixie sighed. "Listen to Trixie. You can't go to Ponyville."

Applejack laughed. "And why shant I go back? Ya hiding somethin'?"

Trixie said nothing. "Just don't get off the train in Ponyville. You were safe in Appleloosa," she said.

"Ya threatenin' me?!"

Trixie violently shook her head. "Listen to Trixie. Don't go back to Ponyville. It's dangerous!"

Applejack ignored her. The train jerked forward and continued moving. Ponies on the train began to cheer as the train sped up. Trixie's reaction was just the opposite. The magician whimpered as the train picked up speed. She got off her seat and walked toward the back of the train. This fueled Applejack's curiosity. Why would Trixie go through all that trouble to tell her not to go to Ponyville? She looked back to see Trixie entering the car behind hers. Applejack sighed and followed the showpony to the back.

When Applejack walked in, she saw several suitcases. She had her hat and cloak on a hat rack, which she began to don. She looked like herself physically, yet she didn't look the same emotionally. Applejack walked over to the magician. Trixie noticed and immediately took a few steps back.

"Ah don't want any trouble, just to talk," Applejack said.

Trixie didn't lower her guard. "Why'd ya say to not go to Ponyville?" she asked.

Trixie rubbed her hoof nervously. "You all made enemies, right?"

Applejack nodded. "Well, Trixie got a letter a few weeks ago. It's something you would not like."

Using her magic, Trixie levitated a scroll from her cloak and opened it in Applejack's face. Immediately, something wasn't right.

Trixie Lulamoon,

I understand that you have a never ending grudge against Twilight Sparkle and her friends. You are not the only one. I have created a team designed to get revenge against Twilight, the Princesses, and pretty much all of Equestria. I know you want to be remembered as the unicorn who beat Twilight, and I can make your dream a reality. Write back your response. I expect a lot from the Great and Powerful Trixie.

-Discord

Applejack's jaw was touching the floor. "Discord? But he's reformed!"

Trixie retracted the scroll. "Trixie wants to beat Twilight Sparkle in magic, but Trixie doesn't want to hurt her. Trixie turned down Discord's proposal and wanted to warn the princesses, but Trixie couldn't. When Trixie heard of Twilight appearing in Ponyville this morning, Trixie knew that today is the day. Day X," she said.

Applejack was at a loss of words. Day X? She looked up at Trixie. "If what ya sayin' is true, then Twilight..."

Trixie nodded. Suddenly, the train jerked to the side, knocking Applejack and Trixie into the wall. The impact almost knocked out Applejack, luckily Trixie stopped her fall using her magic. Applejack looked up at the unicorn and nodded. "Mighty thanks," she said.

Trixie nodded in response. The two mares got up and looked around, looking for any sign of damage. Trixie's ears started twitching.
Applejack could also hear something. Something was going on on the other side of the doors. Applejack opened the doors, and gasped. The whole car was filled with changelings attacking innocent mares, stallions, and fillies.

Applejack looked over at Trixie. Her face said it all. It's starting.

She turned to the magician. "Listen Trixie, ah know we had our differences, but ah need yer help. Help me stop these here changelings!" she said.

Trixie backed away. It was like the Ursa Minor incident all over. She talked the talk, but she couldn't walk the walk. "Listen Trixie, innocent
lives are in danger. Ya gotta help me get rid of em. Please Trixie!"

Trixie sighed and fixed her hat. "Let's go."

Applejack smiled. They both turned their attention to the swarm of changelings. With a loud cheer, the mares charged into the swarm. The apple farmer went for a serious buck in the face of one changeling. The force of the kick sent it into a small group of 10 changelings. They fell like bowling pins. She went around, kicking every single changeling that ever came close to her. Some flew out the window by the power of her kick.

Trixie was having a cleaner fight. Using her magic, she fired several Stun Spells at the changelings, knocking them out. Some changelings took notice and began to charge the magician. She had no choice but to duck and dodge every single one of their charged. She continued to fire spells at the changelings. Some got the idea to use shields against the magician, but she was already one step ahead of them.

Thanks to an idea she got while traveling, she was able to use some gunpowder from her magical arsenal. She had wrapped them up into some cloth, and with a simple flame, she had portable fireworks. She just happened to have some in her cloak. She removed some, and threw them at the changelings. Firing an Incendiary Spell, the bombs caught fire and blinded many changelings.

Applejack was impressed. She reached under her seat and pulled out her rope. She lassoed a changeling, and used it as a hammer against the others. The changelings were smart to duck, well some of them. Some changelings were shot straight out the windows (whatever was left) and into the bog they were passing. She let go of her hammer and lassoed something else: somepony's suitcase.

"Hey, I need th-"

Applejack ignored the stallion as she swung the case. It nailed a changeling in the eye, sending it to the ground. This was a better hammer than a Changeling. She swung and hit as many changelings as she could.

Trixie's magic had greatly improved since her last visit. Using some Transfiguration Spells, she turned changelings into pots of flowers. She was about to nail a changeling with a spell to turn it into a toadstool, but a blast of green energy hit her hat. It was knocked off her head. She turned to grab it, only to see several burn marks in it. The green energy burned right through. Immediately she began to tear up. Her sadness quickly evolved into something else.

Trixie's anger flared. Her magic aura turned red. She started firing magic spells left and right at the changelings. Applejack thought that the fight would soon be over, but the changelings kept coming. She was running out of breath. She couldn't fight forever.

She was knocked toward the window by a changeling. As she wrestled with the changeling, she managed to take a peek at the sky. She noticed something in the distance. Something moving fast and her way. Instantly, she knew who it was. She looked over at Trixie, who was
still firing spells. "Trixie, ah advise ya get down!"

Trixie looked over. She noticed the small streak in the sky behind her. Whatever it was, it was coming in fact. She nodded. She looked back outside. It was getting close. "EVERYPONY GET DOWN!"

All the ponies dove to the floor. Not a moment too soon. Right as Applejack dove for the floor, a large explosion rocked the train. Following the explosion was a bright array of lights. Trixie looked outside to see the lights. Her eyes lit up with the colors. She had never seen anything so beautiful in all her life. No amount of magic could ever mimic it.

The changelings immediately fled the train. Some were immediately met with a pegasi offensive. Applejack had to only laugh. "Ya better run! Ya think the unicorn and earth pony was bad?"

Trixie had to laugh as the changelings fled. When she looked back at her hat, though, her joy was replaced with sadness. Her prized hat was destroyed.

Applejack looked over and noticed Trixie's sadness. She went over to the unicorn to comfort her. That would've happened if somepony didn't interrupt. "Did you see that?! One Sonic Rainboom scared those changelings!" RD said as she flew into the train.
She stopped when she noticed Applejack and Trixie. Trixie was holding back tears while Applejack was comforting her. "Applejack? Trixie?
What are you two doing here?"

Applejack looked up. "Ah was going to Ponyville to see Twilight before all this happened. Trixie found me," she said.

Rainbow looked over at Trixie. "Trixie, did you have something to do with this? Huh? Did you lead the changelings here?"

"RAINBOW!" Applejack yelled.

Rainbow only shrugged. Behind Rainbow Dash flew in Fluttershy. She looked mighty tired from trying to catch up to Rainbow. "Oh, am I interrupting something?"

Applejack didn't have a correct answer. "Look, Trixie is having a problem. Rainbow, ah want you to lead the train to Ponyville. We gotta get these here ponies to safety. Fluttershy, can ya check on the passengers?"

Rainbow Dash saluted and flew back outside. Fluttershy flew in, and started helping ponies up. "Um, Applejack, there's something I need to tell you," Fluttershy said.

Applejack looked up. "Um, I was in Ponyville earlier, and I saw Twilight. She was in her library, and I was about to visit, but something happened."

"What do ya mean?"

Fluttershy took a few steps back. "I, um, I heard Twilight scream."

Trixie looked up. "Sweet Celestia, they got her!"

Applejack and Fluttershy gasped. "You know?"

Trixie nodded and gave Fluttershy the scroll. After a while, Fluttershy began to tear up. That lasted for only a moment. Her sadness was replaced with anger. "How are Discord do this?! HE'S OUR FRIEND! AT LEAST THAT WAS WHAT I THOUGHT HE WAS!"

Trixie nodded. "We gotta get to Canterlot Castle. Ah have a feelin' that's where Twilight is," Applejack said.

Trixie nodded once again. Rainbow appeared at the window. "So we're going to Canterlot?"

Applejack nodded. "Alright, ALL ABOARD FOR CANTERLOT!" Rainbow cheered.

Rainbow flew to the back of the train. Using her strength and speed, she blasted the train toward the small town of Ponyville.

Canterlot

Upon arriving to Ponyville, the girls found the town about ready to tear itself apart from the panic that was the Changeling takeover. When the train stopped at the station, the doors of the cars burst open, spilling ponies of every shape and size onto the platform. Some of the ponies, instead of running around and screaming, charged at the Changelings, ready to defend their home. Trixie elected to get off with the other ponies at Ponyville. She argued that her magic could help them get an edge on the invasion. Instead of agreeing, Applejack argued that her magic could help them get back to Canterlot and fight whatever was attacking them.

While Applejack and Trixie argued about the situation, Rainbow was busy unhooking the train cars from the engine. Fluttershy was at the very front, tinkering with the controls. While she had no professional knowledge with trains and how they work, Fluttershy worked the controls like a professional conductor. This surprised Rainbow Dash as she worked on the last of the cars.

Finally, Applejack gave up arguing with the magician. "Ya sure about this?" she asked her.

Trixie nodded. "Trixie-er I mean I- believe that my business is better here. Besides, I need to fix some broken roads."

Rainbow gagged in the background. Fluttershy gave Rainbow a look that was too perfect. "We need ya help Trixie, but if ya really think this is best-"

Trixie smiled. They clopped hooves and went their separate ways. Applejack boarded the train, but before she closed the door, she turned around to face Trixie once again. Trixie was standing next to a trash can. Her hat glowed in her pink magic aura, and it levitated into the empty bin. Applejack's heart broke. Maybe something could be done. Applejack smiled. She knew what to do. She closed the door behind her, and the train took off.

Thanks to Fluttershy, Rainbow Dash had to struggle to keep up with the train. With no rear luggage holding her back, the Friendship Express blasted through the hillside of Ponyville and toward the royal capital of Equestria. Applejack had to hang onto both her Stetson and a rail just to survive the trip over there.

When the train pulled into the station inside Canterlot, the three friends found themselves in the middle of a war zone. Entire shops were blown up from within. Mannequins with stylish gowns and tuxedos were thrown all over the city streets. Broken glass littered the sidewalks. Guards in full armor were sprawled out onto the ground. Some were alive, some weren't. Fluttershy walked over to one to check for a heartbeat.

She got something different.

As she got close, she noticed something different about the pony. There was no blood, no blunt injuries, no anything to suggest that this guard was involved in battle. The pony seemed to only be passed out. Fluttershy placed her hoof on the pony's head, and that's when it happened. A green glow enveloped the unconscious pony. Fluttershy squeaked and flew back to her friends. Rainbow Dash rolled her eyes.

"Changelings? But how-?"

"I guess we were the distraction," Rainbow said.

Fluttershy hid behind Rainbow. "W-why are th-they here?"

Applejack lowered her stetson. "Ah don't know, but ah would like to find out."

Rainbow smiled. "Let's go ladies! Canterlot is not saving itself!"

"Wouldn't that be amazing," Applejack muttered.

Rainbow was about to fly towards the castle, but suddenly stopped. In front of her was a cage made entirely out of...smoke? The bars were shifting within the darkness, like it was deciding whether or not to be cell bars. The cage had two ponies inside. One was the pompous Prince Blueblood. The other was...Rarity? The fashionista was knocked out on the floor of the cage next to Blueblood. It took all of Rainbow's willpower not to laugh at the sight before her. Rarity would go on rants concerning that night at the Gala when she was treated like garbage by the prince.

Fluttershy flew up and nearly shrieked. "Rarity?"

The unicorn stirred in her sleep. "Not now Sweetie Belle, go play with your friends," she muttered.

Applejack raised an eyebrow. "Ok, A'hm done here. HEY RARITY, WAKE UP!"

Nothing. Rainbow tried rattling the cage, but it didn't move. It felt heavy. "Rarity, please wake up, if you want to," Fluttershy said.

Rainbow rolled her eyes. "The boutique burned down," she whispered into the cage.

In a flash, Rarity was at the cage looking like a maniac. "WHO DID IT? IS SWEETIE BELLE SAFE? WHAT HAPPENED TO MY SUMMER COLLECTION?! I'LL HAVE THAT PONY'S HE-"

Rainbow Dash started laughing uncontrollably. Fluttershy managed a weak smile while Applejack just shook her head. "Nice to see somepony still has her priorities straight," she said.

Rarity looked down at the farm pony. "Excuse me for thinking about my work."

Applejack smirked. "Rarity, what are ya doing up there? Cages aren't your specialty," she said.

Rarity sighed. She looked around, and immediately went into panic mode. "This-this monstrosity! The ugly shades of black and purple just do not make a cage pretty. This horrid craftsmanship is enough of a punishment. Get me out of here!"

Fluttershy flew to the cage door located on the other side. She tried opening it, but found it locked. Rarity sighed. "Well, it could be worse. I
could be stuck in the same cage as- OH NONONONONONONONONO!"

She kicked Blueblood's hoof away from hers. Even when unconscious, he was still an unpleasant pain in the plot. "I don't care how you get me down, JUST DO IT QUICKLY!"

Applejack smirked. She threw her hat down and revealed her lasso. She threw the hoop at the lock on the cage. The cage was heavy enough for it to be almost impossible to move. Suddenly, she felt the cage begin to rock, but only a little bit. Summoning all her strength, Applejack began rocking her body with the cage, struggling not to break her jaw or neck while saving the fashionista.

Applejack could feel the rope started to give away, but she needed it to hang on for just a little longer. The cage was now violently rocking back and forth, throwing Rarity all over the cage. Her mane was all over the place, but not Blueblood's. Figures.

Suddenly, the cage flew off the hook it was hanging on. Rarity grabbed onto the nearest bar, and braced herself. The cage hit the ground, and cracked the pavement below. The loud echo of metal slamming into the ground rocked the dead quiet city. The cage door slowly opened, and Rarity flew out faster than Rainbow Dash could make a Rainboom. Speaking of Rainbow, the cyan pegasus was still laughing her mane off at the sight before her.

Rarity growled like a lion, but sighed. "Thank you Applejack. Although, when I say 'I don't care how you get me down', you should consider that I mean 'Get me down from here posthaste without damaging my mane'."

Applejack rolled her eyes. "Nice to see ya too Miss Prissy."

Rarity smirked and hugged the earth pony. "Applejack, where ever did you go? You disappeared from Ponyville, and everypony was worried."

"Ah needed to travel. Ah was just bored with tha scenery," she said.

Rainbow nodded. "Feels good huh?"

"Mighty so. But, ah missed the family. Ah heard Twilight was in town so ah hopped on a train to get here."

Rarity perked up. "Twilight? Twilight was in Ponyville?"

Fluttershy nodded. "This morning I was going to pick some flowers for Angel, and I saw Twilight run toward the Library. She seemed busy, so I didn't go talk to her," she said.

Rarity smiled. "And dear, I do apologize for missing our spa days. I promise to make it up to you in the future."

Fluttershy smiled. "You don't have to do that-"

"Oh, but I insist. And to make it up to you, once this is all over, I will treat everypony to a grand day at the spa here in Canterlot. You thought the Ponyville spa is amazing? Wait until you try-"

"Ah, girls, ah think that's enough," Applejack said.

Rarity chuckled. Rainbow went to check on the knocked out Blueblood. He didn't move nor speak. He was out cold. "I don't think Blueblood is waking up sometime soon," she said.

The girls all agreed and proceeded to move. All of a sudden, thunder clouds rolled into the city. The wind started to howl in the day. A crash of thunder scared Fluttershy to the point of unconsciousness. Luckily, Rarity was there to help calm her down. They all were.

Rainbow landed on a pile of rubble to avoid the winds. They were picking up quickly, and these clouds were moving on their own. A crash of thunder followed a blast of lightning. The bolt pierced the clouds, and a chariot was seen flying towards the city of Canterlot. The ponies all backed away as the chariot got closer. Behind the reins was a pony in a black cloak.

Fluttershy backed a bit farther than the rest. She suddenly stopped when she realized something was behind her. She turned around, and there was her now ex-best friend: Discord. He gave her a small wave. "Why hello Fluttershy, it's been a while."

Fluttershy stood in shock and anger. "Discord? So it is true! You decided that, even after we forgave you for everything you did, it was a good idea to do this? To turn against your friends?"

"Where's the fun in being good? It's so much better being bad," he said, donning a curly mustache seen on the faces of movie villains.

Her blood began to boil. She launched herself at Discord, but he disappeared in a flash bang. Fluttershy landed face first into a potted plant. The group turned to see Fluttershy eating daffodils. They heard an echoing laughter from their favorite Draconiquus as the scene in front of them turned into smoke.

"Discord! Ya two-faced traitor!" Applejack yelled.

"Bring it on, Discord! I've always wanted to do this!" Rainbow shouted.

The smoke died down. In front of them was the cloaked pony. They all knew who it was. The hood came down, and the face of Nightmare Moon was burned into the minds of all the ponies. "Well, look what we have here. The 4 ponies who stripped me of my power. That failure will be made up here, tonight."

Nightmare V. Discord

The four friends stood back as Nightmare Moon appeared. Fluttershy was the most worried. Behind them, Discord was there tossing up an emerald like a bouncy ball. That's because whenever it hit the ground, instead of shattering, it bounced back into his paw. "I thought you all liked surprises," Discord said. "Looks like I was wrong."

Rainbow flew up into Discord's face. "Listen here, buddy! You are going to reverse all of this right now before somepony gets hurt! I thought you were reformed!"

Discord rolled his eyes. "There's reformed, then there's acting. I never liked the princesses, and showing them that I had 'changed' made it easy for me to create the perfect storm!" His form changed to an attire found in the 1600s England. In his paw was a foam skull. “I should take up acting.”

Fluttershy flew up to Discord. "You lied to us! You never cared about being our friend! You are just one great big MEANIE!"
Tears formed in Discord's eyes. "Fluttershy, I am so sorry. I promise you will never see this side of me ever again. Please, can you forgive me?"

As if on cue, Nightmare fired a beam of magic at Fluttershy. She shrieked as she fell to the ground. Rainbow rushed down to help her friend.

"Fluttershy!"

The others rushed to Fluttershy's aid. Rainbow helped her friend to her hooves. "Um, thank you, um..."

Rainbow was confused. "Um, Fluttershy, are you OK?"

The pegasus nodded. "I don't know why my eyes are still clos- oh no."

Rarity moved closer to the pegasus. Fluttershy cowered and dropped to the ground. "Why is everything so dark? Oh Celestia, I-it's so dark. Ple-please somepony turn on a light."

Rainbow looked at her friends. "Sweet Celestia, my eyes are open. I can't see! I'm blind!"

The group gasped. Rainbow turned to Nightmare Moon. "You give my friend's eyesight back, or I'll-"

Discord snapped his fingers. Instantly, an apple lodged itself into Rainbow Dash’s mouth. With another snap of his fingers, two anchors wrapped in chains ensnared the pegasus, sending her straight into the ground. The fall forced her to take a bite from the apple. Applejack was the next to take action. She readied her rope, and attempted to lasso the Draconiquus.

It didn't work.

The lasso immediately turned into a snake. The snake hissed at the Earth Pony, forcing her to drop it. Rarity was busy trying to free Rainbow from the anchors. The process would've been quicker if Rarity didn't use a Hoof Filer to cut the chains. Fluttershy was still cowering behind Rarity.

Discord sighed at the sight before him. "Maybe this is a bit too easy," he said.

Nightmare looked at him. "And yet you were defeated by these pests...twice! You think this too easy?"

"Well look at them. One is blind, the other is weighed down, one is defenseless, and then there's Rarity. Believe me when I say that Rarity doesn't have an offensive abilities except for magic. I've seen what she can do, but that only applies with fashion. Face it, Nightmare, this is too easy," Discord said.

Nightmare facehoofed. "Well maybe it is without the Elements of Harmony. I thought you said the Elements were in Ponyville!"

"I told you, and you looked everywhere except where they are. You were probably standing right on top of it and didn't notice!"

"What is thou saying about thee?! That I be a blind fool?"

Discord cracked a smile. "If that's what you want to call it, sure. You 'be a blind fool'."

"TIS A LIE DISCORD!"

"Says the pony who knew Celestia had control over the Elements of Harmony! You knew the Elements were her new weapons, and you didn't bother trying to eliminate them? Face it, you be a blind fool!"

Nightmare's horn lit up. "How about I correct a small flaw in this plan!"

Discord summoned two Chaos Cannons: devices that were able to spread chaos anywhere and everywhere without wasting energy. "Bring it on, Moon Butt!"

Nightmare fired a magical beam at the god of Chaos. He simply dodged it and fired one of his cannons at Nightmare. A direct hit on the snout gave Nightmare an uncontrollably growing mustache and beard. Another shot fired and gave Nightmare a DUNCE hat.

Nightmare formed a pair of scissors and snipped the beard and 'stache. She shook the cap off her head. She fired a magical blast at Discord's Chaos Cannon, turning it into a bunch of bats. Discord rolled up his imaginary sleeve. "Oh it's on!"

With a snap of his fingers, Nightmare's wings turned into Jell-O. A pink cloud of chocolate milk rained down on the Princess of the Night. Her facial expression said it all: you've got to be kidding me. Discord reached over and plucked Nightmare's horn from her head and used it to scoop up the cloud. At first, Nightmare had no idea how to react. She just punched Discord, forcing him to drop her horn.

Discord sat straight up and summoned a glass of chocolate milk. He threw it at Nightmare's head, luckily she managed to duck in time. The glass flew over her head and exploded behind her. Nightmare turned her head to the crater left behind. Inside was a couple of Jack-in-the-Boxes crawling out and breaking into shops nearby.

Nightmare charged her counterattack. She fired a beam, hitting Discord's cloven hoof. Immediately he was engulfed in a black smoke. He shrieked as the smoke encased him. Nightmare fashioned a victorious grin. "Would'st thou apologize for thy offensive comment about thee?"

Discord laughed from within. "No way, Jose!" he called out.

Nightmare's victorious grin changed to a confused look. "And who is this 'Jose'? Is he one worthy opponent?"

Instead of answering, a block of ooze flew out of the smoke, nailing Nightmare in the muzzle. The cloud disappeared, leaving one dazed draconiquus behind. He looked over at the alicorn. She was covered in the ooze that sailed through the sky. Discord walked over and leaned into her face. "Checkmate, Nightmare."

Nightmare sighed in defeat. "Perhaps thou art correct. Perhaps this affair in Canterlot is too mediocre. A complete victory is control over the Elements," she said.

Discord allowed the ooze to melt, allowing Nightmare to stand. "I suggested looking in Ponyville. I said that a billion times!"

"The Elements are not there. There is none there but workforce," she said.

Discord sighed. "Twilight hid them in her library! There are in a glass case, and-"

Nightmare raised her hoof. "Where are the ponies we had reigned victorious over?"

"They're right over he-"

He gestured to the spot where the 4 ponies were, but the only things that were in their places were a bunch of chains, a snake, and a knocked out Prince Blueblood. Discord's jaw dropped to the floor, clanking like a piece of metal. "That's not fair," Nightmare said.

Discord sighed. "And that's why ponies are the worst to lock up and forget."

Canterlot Castle Mayhem

Rainbow hated being the rescued. She could've taken on Discord and Nightmare Moon without any struggle, even while weighed down. With Discord and Nightmare arguing on how easy their takeover was, Rarity unlocked the chains on Rainbow Dash's hooves, picked up Fluttershy, and took off. The girls followed suit.

Applejack's mind was still racing. Discord, the draconiquus who they showed tolerance to, had betrayed them. It was expected, obviously, but for him to stand by and watch as Fluttershy loses her mind and nearly have a heart attack was too much. She felt like a disappointment. It was because of their combined power that Nightmare Moon fell, but now she was alive and ruler of the world. To know that their first night as friends proved nothing more than the fact that 6 different ponies can meet and call each other friends.

Rarity, being the unicorn who spent a lot of time roaming the castle, knew all the twists and turns they needed to take. She led them through hall after hall after hall. Along the way, they managed to run into some changelings. Applejack's hind leg strength proved to clean changelings easy.

Rainbow Dash sighed as they reached another endless hallway. "I could've taken those two without breaking a sweat," she said. "We should've stopped them while we had the chance!"

"Rainbow! Nightmare gone and blinded Fluttershy and weighed ya down on the ground. Mah rope turned into a snake and Rarity doesn't have combat spells," Applejack said.

Rarity shrugged. "I never did like the style of offensive magic. I mean, who would think using magic in such a cruel way would be acceptable?" she said.

Applejack shrugged. Fluttershy stayed silent. She was too afraid to speak in darkness, even if it is just her vision that is obscured. Rarity panted. "Anypony else want a turn?"

Applejack trotted over to Rarity and offered to take her for the time being. Without Fluttershy on her back, Rarity was able to stretch for the first time since the cage fell earlier. Applejack centered Fluttershy on her back, and they continued walking/flying. Occasionally, Rainbow would quickly spin around to see if anypony was following them.

Fluttershy once walked in on one of Twilight's many lectures to herself. She once heard that if one sense is obscured, the other 4 will become stronger. Without her vision, Fluttershy was able to tell how far the hall went. She heard the collective voices of Rarity, Rainbow, and Applejack. She was also able to pick up a faint whisper. Her ears twitched as she looked for the sound. The whisper was calling out to her. It was a collection of whispers all saying the same thing: turn left.

Fluttershy didn't say a word, but then she heard something else. A voice she recognized all too well. "Left."

The trio stopped. "Um, what?" Rarity asked.

Fluttershy shrunk down. "Um, if it isn't too much trouble, I think we should turn left. That is-if you want to."

Rarity smiled and turned to the direction. Down the small corridor was a door. A single door, and it was ajar. Rainbow could swear she saw somepony move behind the door. Instead of silently checking it out, Rainbow burst toward the door. Rarity was too slow to use her magic to stop her.

Rainbow blew the doors wide open. The room inside was empty. A couple shelves of books lined the wall with several thrown about. A couch was turned upside down in the far right corner. A large stone was propped up against the nearby wall. In the middle of the room was a bejeweled box.

"Rarity, Applejack, come check this out!" she called out.

The two walked in. Fluttershy was busy humming to herself to calm her down. It seemed to be working since she had a grin on her face. "No way. Sugarcube, ya found the Elements!"

Sure enough, the chest containing the Elements of Harmony was sitting there on top of a pedestal. The box opened, revealing 4 necklaces.
The girls gasped. Pinkie's Element was missing. Since Twilight used her Element as a crown, it was more than likely with her. Rarity levitated the Elements to the girls before she put hers on. Before she did, however, Pinkie happened.

There was a loud battle cry. Rarity just had to look up to see Pinkie falling from the ceiling. Rarity was too late to react, and was immediately squashed by the bouncing pink pony. Two mysteries were solved at that moment: the case of the missing Pinkie and the disappearance of the Element of Laughter. Fluttershy did a quiet giggle before she felt somepony staring at her. Applejack flat out laughed at the scene before her. Rainbow was laughing out loud while struggling to stay airborne.

Rainbow helped Pinkie from Rarity, who was about ready to get her hooves dirty for a bit of payback. "Pinkie, what in the name of sanity were you thinking?" Rainbow asked.

Pinkie shrugged. "Had to see if she is a changeling," she said.

Rarity sighed. "Darling, you didn't have to drop from the ceiling just to see if I was a changeling. I am not a changeling," she said.

"Prove it."

Applejack facehoofed. Rarity sat there pondering ways to prove to Pinkie that she was the real deal. "Um, when we were stranded in the desert, thanks to somepony, I was questioned on whether to call your new treat a Chimicherry or Cherrychanga. We spent a good few hours in the desert debating over the subject before we caught a train to Ponyville." She paused. “We decided on Cherrychanga by the way.”

Pinkie leaned into Rarity's face. Rarity could feel the party pony staring into her soul. "Okey-dokie!" Then she hopped away.

Rainbow watched as Pinkie left. She was about to say something, but shook her head and flew out the door. Rarity looked up at the ceiling.

"How did she ever get up there?"

"Beats me. Ah never question Pinkie anymore, not since the Mirror Pool thing," Applejack said.

"Or the pre-birthday party for Angel," Fluttershy said.

Applejack sighed. "Poor Angel. Is therapy doing OK?" Rarity asked.

"Oh yes! Angel has made progress, but I cut out the cucumbers in his salads. We don't want to have him remember the party," Fluttershy
said.

Rarity began to remember the party, and shook it out of her mind. Only Pinkie can find a way to shove 15 cucumbers in Angel's mouth with a candle at the end of each. Applejack fixed Fluttershy on her back and began to walk out the door. Before she did, however, she noticed something on the corner of her eye. A creature was in the corner of the room. It was an adult-sized animal. The animal was sandy colored and seemed to be staring at the Earth Pony. Applejack ignored it and closed the doors behind her using her tail.

Pinkie was full of surprises as time progressed. Somehow, she had hidden a party cannon and pulled it out whenever a changeling looked their way. At the press of a button, the changelings would be covered in so much confetti, that it was impossible to get it out. Rarity was stunned at the Earth Pony's actions.

The 5 finally came to the main hall. The doors in front of them were giant and without any guards. Applejack fixed her stetson. "Y'all ready?"

The 4 nodded. She took a deep breath and kicked open the doors. The scene inside was horrible. Queen Chrysalis and King Sombra were sitting at the throne of Celestia. Several changelings and shadow ponies surrounded the two monarchs. In the middle of the room was an injured Princess Celestia. Her horn was snapped in half. Above her was Twilight.

The recently crowned alicorn had an energy shield over herself and Celestia. Changelings were seen trying to find a way inside along with what appeared to be Shadow Ponies. They hammered at the shield with no success.

Sombra was laughing as the doors opened. He looked up and with a magic spell, cast a bright light over the 5. The girls screamed in terror as they felt pain erupt all over their bodies.

"Well, it looks like we have some visitors," Sombra said.

Shadows have closed

Twilight was happy to see her friends again.

Ever since her visit to the human world, Princess Celestia and Luna sent Twilight all over Equestria to be better familiar with the realm. Her 3 days in the human world opened many doors for her and the royals. With new knowledge and possible goals put in place, Twilight needed to be sure everything for the future would be perfect. Unfortunately, she overlooked Discord’s free time. Because of the limited restrictions on the draconiquus, Discord had managed to recover Sombra and Chrysalis. How Nightmare Moon survived was a mystery for all of them.

When she had awoken from her sleep, Twilight immediately searched for Princess Celestia. After finding the Princess of the Day, the two decided to take on Chrysalis once more. With new spells in both of their arsenals, they thought they were finally going to win without the Elements. They thought wrong.

With the appearance of Nightmare Moon, Celestia’s guard was lowered. A magical burst of dark magic quickly incapacitated the princess. Twilight, however, studied various combat spells from Starswirl’s journals. His extensive research on the matter proved to be helpful, yet she was limited. Much of the offensive magic she learned either evolved into different forms of magic, or were labeled as duds. Because of that, she was put on the defensive.

Twilight held the shield up against the Changelings. Nightmare, after realizing that she had no minions of her own, crafted Shadow Ponies to fight in her name. With Luna away on official business outside Equestria, no help was coming. She then summoned and ordered the Shadow Ponies to wreck Canterlot and then, just for fun, attack the Princesses. They cackled when they were given their mission.

The doors burst open and Twilight felt happiness for the first time since the nightmare started. Her happiness fell into dread as she watched her friends overpowered. Her relieved emotions suddenly turned to dread. She nearly lowered her shield, but she stayed strong for both her and Celestia’s sake. Sombra looked over and chuckled. “I don’t see the threat that Nightmare told us about,” he said. “All I see are 6 very scared ponies and a sorry excuse of a Princess.”

“It’s hard to imagine that these 6 defeated us. At least Discord had the right idea to separate the Elements the first time around.” Chrysalis said. “So, what do we do with these 5?”

Sombra looked over at the 5 ponies sprawled out on the floor. “Well, the concept of ‘Divide and Conquer’ sounds like the best way to execute this.”

Chrysalis smiled. She walked over to Applejack, who was chained by the hooves. “I never did like those cursed Apple Fritters you fed me. They were just disgusting.”

Her horn glowed green and Applejack was bathed in the light. When it subsided, Applejack was on her hooves, bowing before Chrysalis.
“Applejack!” Rarity shouted.

Sombra immediately spun around and eyed the unicorn. “Silence!”

She immediately did so. Chrysalis and Applejack returned to the throne. The earth pony had no emotion in her face, and that worried Twilight. “Now, are you going to surrender, or am I going to have to pick a henchpony myself?” Sombra asked.

Twilight looked over at her friends. They were all saying the same thing: don’t do it. If I surrender, maybe Applejack can be saved, Twilight thought.

The alicorn sighed and dropped the shield. The minute she did so, a Shadow Pony knocked her halfway across the room. She hit a column and slumped to the ground. Chrysalis laughed like a hyena. “Restrain her,” she ordered.

A changeling and Shadow Pony flew over and pinned her to the column. Sombra sighed. “Finally, ultimate victory.”

Rarity growled at her captors. “This is not how one treats a lady! I demand a better method of detainment!”

Sombra chuckled. He walked over to Rarity, and with the space between his horn and hers closing, Rarity felt fear engulf her. She shut her eyes, expecting the worst from him. In a flash of light, Rarity was let go. She wiped her eyes and turned to Rainbow Dash. Her eyes were green with a dark magic aura surrounding her horn. “RARITY!”

Sombra laughed. Rarity cracked a smile. “Oh wow, all this freedom! All this vast knowledge of the dark and artificial! This magic is more powerful than that of Celestia! I see why you used dark magic, Twilight. Dark magic is just so much easier to use than anything else. There are no rules for it! This is marvelous!”

Twilight looked up and felt dread. “But-but I surrendered! You leave my friends alone!”

Sombra looked over at the alicorn princess. “I never said I wasn’t going to use them. I just got you to lower your shield. Remember child, you brought this upon yourself!” he said.

Rainbow grew angry and tried flying to rescue her friends, but suddenly, her wings felt heavy. Her wings fell to the ground along with her. She looked over, and realized that her wings became solid crystal. She tried getting to her hooves, but her wings were too heavy. She was trapped. Pinkie and Fluttershy were bound and tied by a Changeling. “What possessed you to join forces?” Twilight asked.

“Discord,” Sombra said.

The draconiquus poofed into existence next to the king. “You called?”

“With Discord’s guidance and carefully thought out plan, we finally stood a chance against all of you. It is true that Nightmare Moon brought you all together, but it was Discord who discovered the weakness in the Elements: if one was inactive, then all of them are useless,” Sombra said.

“By my power, I defeated Princess Celestia, but your brother was the one who humiliated me back during the wedding. Lucky me that he has to protect his new home first beyond anything else. I’ve sent some of my children to the Crystal Empire to distract them,” Chrysalis said.

“And by my power, I finally defeated the Empire. I’ve sent some Shadow Ponies, by the permission of Nightmare of course, and managed to corrupt the Crystal Heart. One puny distraction has turned into a perfect victory!”

Twilight tried moving, but her captors were too strong. “You know, I’ve read a lot of books about villains who talk about their plan and expect to get away with it, but it will never happen. Because you told me everything, I now know where to look and how to win,” she said.

Sombra laughed. “If you can escape, then we’ve made a mistake. C’mon then, Twilight Sparkle, try to find help. You won’t find any,” he said.

Twilight smiled and shut her eyes. Her horn began to glow and her captors were turned into bunnies. Discord looked on with amusement. Twilight ran to the middle of the room and grabbed her Element of Magic. “My magic has doubled with the Element of Magic, Sombra! I can still beat you!”

She charged up her energy. Sombra sighed and played along. The two opened fire on each other. Their magical energy met in the middle of the room, bathing everypony in a bright light. Sombra was noticeably struggling under the Element’s power. The beam inched closer to
Sombra’s horn. If their magic collided at his horn, he would be broken into pieces again.

Chrysalis tried stepping in, but was blocked by Sombra. “I can do this! I don’t need help from an insect!”

“An insect?! How dare you!”

Chrysalis fired at Sombra, causing him to lose his concentration. Twilight was now an inch away from victory. Chrysalis noticed this. “Looks like the King of Fear needs help,” she said. She then added another beam of magic into the mix. Twilight tried adjusting to the new source of magic.

She couldn’t make it.

The power of combined magic against hers was too powerful. Her magic gave out, exposing her Element. The dark magic overwhelmed her, sending her out the window and into the dark abyss below the city.

“TWILIGHT!”

Welcome aboard

Rainbow struggled to move. The memory of Twilight being blasted through the window was replaying itself in her mind. Each playback was worse than the last. Tears were forming in her eyes as she cursed at them for the first time in her life. Sombra smiled at Rainbow’s anger and sadness and even produced a camera to record her cursing. Rarity and Applejack remained emotionless in the middle of the throne room. Behind her, Pinkie was as silent as the grave while Fluttershy begged for her vision back.

Chrysalis sighed. “As much as I wanted her gone, this was not what I expected at all,” she said.

Sombra looked over. “If we decided to let her live, she would’ve found a way to overcome us. Her demise is necessary if we want Equestria all to us,” He said.

Chrysalis rolled her eyes. “Well then, with no more heroes of Equestria up your sleeve Celestia, it looks like this is victory,” she said.

Princess Celestia raised her head. Her horn, still broken, started to run a familiar red liquid. Her face drained of color from exhaustion. “You haven’t won yet, Chrysalis. Remember, there are millions of ponies who will do whatever it takes to keep their families safe. You hit too close to home. Expect a revolution,” she said.

Chrysalis smiled. “Guards, lock her up. Send the yellow and pink ones to the dungeon! May they never see the light again,” she said.

A few Changelings walked over and carried the two ponies away, against their protests. Rainbow tried flying, but her crystalized wings were too heavy for any kind of movement. “Girls! Don’t worry, I’ll get us out of here! Fluttershy, don’t be afraid!” she called out.

The door closed behind the prisoners. “And what of the rainbow one?” Sombra asked.

Chrysalis smiled. “Discord, have her sent to the Everfree Forest. Let her play with the monsters inside,” she said.

Rainbow puffed up her chest. “I’m not afraid of the Everfree! I’m brave enough to take on anything in there,” she said.

“Your bravery only comes when you can run. Goodbye Rainbow Dash.”

“Traitor!”

Discord snapped his claws, and Rainbow disappeared. Sombra laughed at her disappearance. “Now, Miss Rarity, I have an empire to return to, and I need somepony as my First General. Will you be willing to fight in the name of Your Highness?”

Rarity smiled. “But of course,” she said.

Sombra smiled and teleported out of the throne room. Rarity followed suit. Chrysalis looked down at her slave. “Oh young Applejack. So very young and filled with sadness. You will be remembered beyond Twilight Sparkle. I have a pest problem at the apple orchards, and my Changelings need help resolving the problem. How would you like to help your queen?”

“Ah would be delighted,” she said.

“Good, now go. Your commanding officer will lead you to the first orchard.”

Applejack turned and walked out the door. Chrysalis smiled. Finally, victory!

*Beep beep beep*

The sound of a heart monitor slowly rocked Twilight back into consciousness. Her eyes slowly began to open, taking in her surroundings. She was in a hospital, a really weird hospital. She looked around. It was a single room and only one bed, and she was in it. The heart monitor was on her side, showing her that she is alive. She raised her head, only to be forced back down by pain. Her hoof instinctively ran up to her head. Bandages. She felt something warm underneath her bandages, and she guessed that it was blood. She groaned and slowly rose up.

Another painful shot ran up her head. This time, it was at her back. She looked over to see her wings bound to her body. She could only imagine her wings were broken. 3 months of having wings, and I break them. And how is Spike still well enough to be my assistant?

Her eyes shot open. Spike? Spike! She looked around, looking for her baby dragon. He wasn’t there. Her heart monitor began to beep rapidly and she knew there would be a doctor coming in to check up on her, but that didn’t matter. She needed to find Spike.

Immediately, the memories of what transpired in Canterlot flooded her mind. Rarity and Applejack becoming slaves of Sombra and Chrysalis, Fluttershy being blinded, Rainbow bound and helpless, and Princess Celestia near the point of death. She remembered trying to fight back with her Element of Magic, but it failed her. She thought she would win with her Element on her side, but nothing helped. She was blasted out the castle and her friends probably think she’s dead. Pony feathers, she thought.

She looked over at the counter next to her. Her Element was there, but the jewel was cracked. She read that cracking an Element was impossible, but it looks like it happened. They won. I can’t fight back, not without the Elements.

A hoof rested itself on her shoulder. She looked up. Princess Luna was there with a sympathetic look on her face. “Twilight Sparkle, it is good to see you alive,” she said.

Twilight was at a loss of words. Instead of a simple ‘Thank you’, Twilight rose up and hugged the Princess of the Night, completely ignoring the pain she was experiencing. Luna was taken back at the sudden display of affection, but she hugged back. “Luna, I’m so sorry that I couldn’t protect her. They have Princess Celestia. I’m sorry. I let you down.”

Luna pulled the Princess of Magic back. “You did the best you could. You defended her while I could not. I am grateful that you were there for my sister.”

Twilight nodded and pointed at the Element of Magic. “What do we do about the Elements? Mine is cracked.”

Luna looked over at the crown. Twilight saw a spark in her eyes as she studied the cracked gemstone, almost like she had a plan. “I think I know somepony who can help you with this. He is here with his assistant. I am sure he knows what to do,” he said.

Twilight looked up. “Is it Starswirl?” It was a farfetched question, but nopony else really understands the Elements as much as Starswirl. “I mean, perhaps Starswirl had something specific about how to fix a cracked Element or something. Perhaps maybe some ancient texts?”

Luna shook her head. “No, but he is close. He is as clever and wise as Starswirl. I will take you to him.”

Twilight nodded. She jumped onto the floor, and sparks of pain flared up in her back. She made a mental note not to do something stupid like that just after waking from an injury that nearly cost her life. Once the pain subsided, the room began to shake. The shaking threw Luna and Twilight off balance. “I think that’s him now,” Luna said.

The Princess of Magic was confused. Were they in a traveling hospital? She followed Luna out of the hospital wing. In the hallway, there were engravings of strange symbols on the walls. They were not like the runes she studied from Pre-colonial times in Equestria. These were circular. In fact, these runes looked older. Older and more powerful. Twilight made a mental note to study them later.

They reached the end of the hall. In front of them was a pair of gold doors. “I must warn you, Twilight Sparkle, he is a bit eccentric. Patience is key with him,” Luna said.

Twilight was confused. “Who is he? A magician? A scholar? A scientist? A doctor?”

Luna smiled. “All of the above.”

The Princess of the Night opened the door. Twilight’s eyes couldn’t open any wider. She was in a very large room lined with copper. Frames extended from the floor all the way into the ceiling. In the middle of the room was a giant console with a large green tube running up to the ceiling. At the console was a brown Earth Pony with a messy mane. Next to the Earth Pony was a familiar gray Pegasus. She recognized the Pegasus from some of her endeavors. It was the mail mare who crashed into her balcony with a gift from Princess Celestia.

The room continued to rock back and forth. The console began to explode, and the earth pony was trying to fix it. He flipped switches and pushed buttons at an unnatural speed. She looked up at Luna with a confused look.

Luna smiled. “Don’t worry, he is a genius,” she said.

Twilight looked back at the earth pony. He stopped and looked in their direction. He told the Pegasus something and walked over to them.

“Luna, I can see you got bored with the library,” he said.

“It’s in the pool Doctor. I had to leave to avoid ruining your collection,” she said, holding back a chuckle.

The words ‘Library’ and ‘Pool’ in the same sentence didn’t seem compatible to Twilight. Why would the library be in the pool? The earth pony looked over at Twilight. Immediately, she recognized him. He would always be around whenever she or her friends got in trouble. It was him and the Pegasus who were there when she had to settle a dispute with the Appleloosans and buffalo tribes. He was there when Nightmare Moon returned. She ran past him when he was asking a question.

The stallion turned to the lavender princess. “I see our patient decided to join the world of the living.”

Twilight extended her hoof. “My name is Twilight Sparkle,” she said.

He smiled. “Nice to finally be introduced to you, Twilight. I’m the Doctor.”

“Doctor who?”

“Just ‘The Doctor’,” he said.

Twilight raised an eyebrow. Before she could question him, the room jerked forward. The Doctor turned to the Pegasus. “Ditzy, ease up on the controls! We aren’t jumping into the Vortex this time!”

“I’m not trying to. They found us Doctor!” Ditzy called out.

The Doctor’s eyes widened. “Alright then, it looks like we aren’t staying here. Off we go!”

He ran back to the console. Twilight and Luna followed. The Doctor noticed them both. “Luna, I need you to keep that lever in the midway position! Twilight, press that blue button whenever it turns red. Ditzy, I need you on the shield. They are hitting us with everything they got!”
Luna and Ditzy ran to their stations while Twilight did nothing. The Doctor looked over to her. “Oh, and welcome to the TARDIS. Allons-y!”

The Doctor flipped a switch, and the TARDIS jerked forward. Twilight clung onto the console. She pressed the button as instructed. The Doctor and Ditzy were cheering. Luna was smiling while Twilight was starting to feel sick.

I must be dreaming.

Author's Note

I'm keeping my promises. I'll have another chapter up soon. Flutter On!

Mayhem in the Control Room

One of the many things running through Twilight’s mind was, Am I dead? The answer was obviously no. She was in a huge copper control room with a giant tower of nonsense with a stallion who has no name, a wall-eyed mail mare, and the Princess of the night. The lavender alicorn knew nothing of what was going on, but Luna trusted the stallion.

The room rocked back and forth as the Doctor continued to speak gibberish. It seemed as though Luna and Derpy knew what he was talking about, which was impossible in her case. The Doctor threw a switch, and the entire room began making a noise. A loud screeching noise that raised the hairs on Twilight’s coat. Luna reacted by throwing the same switch back in its original position. “We do not need to obliterate Twilight’s hearing,” she told the Doctor.

“Right, I’m going to have to fix that. I don’t understand, I changed the Extrapolators a long time ago,” he said.

“How long ago?”

The Doctor hit his head on the console. “Um, about a few minutes after you dropped Twilight off,” he said.

Luna face-hoofed. Twilight looked down on the switches. The console was literally littered with bells, whistles, and sticks. Twilight pressed a button to only have the Doctor freak out. “Do you want to open a rift right above Canterlot?!”

Twilight looked up in shock. “A what?”

“A hole in the fabric of reality. A tear where time and space spill into the physical world. Opening a rift and not having the right stabilization could very well contaminate half of Equestria with pure Time Energy, and if a proper defense isn’t in place, that half of Equestria will be lost forever. Do you want a tear in time and space to open up in a dense populated area?!”

Twilight’s eyes widened. “No, not at all!”

The stallion fiddled with a few switches before resuming his work at the console. The entire room shook again as another explosion rocked them. “Grah, they’re hammering us with everything they’ve got. I can’t do anything when one part of the console is on the other side of the room!” The Doctor said.

The alicorn stood there as the Doctor continued to run around the console with his companion in tow. Derpy looked over at Twilight, and pointed to the switch that was shaking. Twilight shrugged to herself and moved the lever. Immediately the room began to stabilize. Twilight could feel her heart beating louder than ever before. The Doctor looked over to where Derpy was, and chuckled. He continued flipping more switches before he stopped.

He was about to rest on a chair, but the room jerked forward again. “Shields are fading fast! I can’t get us out of here! It’s like there is a magical force field surrounding the planet, making it completely TARDIS proof,” the Doctor said.

Twilight looked over. “TAR-what proof?”

“TARDIS. Stands for Time and Relative Dimension In Space. It’s my time machine,” the Doctor said.

Twilight looked at him for a moment. “You’re joking. This cannot be a time machine. That technology is impossible.”

“Yet there are Time Spells in the Royal Canterlot Archives in Starswirl’s Wing,” he rebutted.

“But that’s just magic. You don’t have any knowledge of magic. Unless you are hiding a horn under your mane, you cannot possibly travel through time!”

The Doctor smiled. “I would love to prove you wrong, but right now we need to get away from the Shadow Ponies chasing us. Derpy, what’s the status on the shields?”

“They’re going down fast. The glass thingy is saying 9 power,” she said.

“9% power left? I thought I had more. Oh well, that’s what happens when I have the shield on while playing Bowling for Asteroids. OK, it is obvious that the Shadow Ponies are stopping us from hitting space, but why? Let a blue box escape into the outer regions of the planet. What could it be?”

The mares stayed silent as the room shook. “What’s changed since we came back here?”

Luna searched her mind. “Nightmare Moon’s power could have encased the planet to ensure nothing escapes,” she said.

“That is true.”

“But this is fairly new magic. With a machine like yours Doctor, and with the right maneuvers, we can get past the shield before it completely covers the planet.”

“I’m afraid it’s too late for that. See, when Nightmare Moon first spawned into existence, she distributed so much dark magic into the castle that it latched onto any source of darkness. Her power gave life to the shadows, but that wasn’t enough for them to grow, until…”

“The Summer Sun Celebration a year ago!” Luna shouted out.

“Correct. Nightmare Moon returns, and without Princess Celestia, the night time lasted a good 5 extra hours. Nightmare disbursed her magic all over Equestria, even latching a part of her life force onto a shadow for protection. She knew the Elements would be used once again and plotted against death. Nightmare Moon had secretly bided her time and allowed her own magic to quietly encompass the planet.”

“But that doesn’t help us against the Shadow Ponies,” Derpy said.

“Aha! But it does. Princess Luna returns with renewed ambitions to adapt and accept her role as Princess of the Night, leaving all that dark magic in the hooves of Nightmare. She rose an army against the Elements and soon had enough power to rise again,” the Doctor said. “She grew a new army of living shadows to stop the Sun.”

“They are keeping us from leaving Equestria. The Shadow Ponies must think we are a threat,” Luna said.

The Doctor nodded. Meanwhile, Twilight was trying to build the picture. “Dark magic has encased the planet!”

The Doctor nodded. “And getting past that much dark magic requires an equal amount of light magic. Luckily, we have two alicorns who are both gifted with extreme magical skills.”

Luna and Twilight both exchanged glances. They silently realized what to do. Luna poured all her magic and energy into her horn, and so did Twilight. Immediately, their horns began emitting large amounts of magical energy. The console began to glow lavender and purple. The Doctor stood back along with his companion. Immediately, the TARDIS jerked forward, but not by the Shadow Ponies. The switches that the Doctor threw were going back to their original positions as the TARDIS accelerated.

Derpy began hovering in the air while the Doctor was taken for a roller coaster ride. The two alicorns continued focusing all their energy into flying the TARDIS, despite the rocking control room. Twilight knew that, in order to focus all magical energy into a complex task, she needed to think happy thoughts. Immediately, her mind reeled back to her first day with her friends. The day after the Nightmare Moon fiasco. Pinkie had staged a more ‘formal’ party welcoming her to Ponyville. She also remembered seeing Princess Celestia and Luna on her first week in Canterlot. She spent an afternoon with Princess Luna and tried teaching her the ways of the new age.

Her mind fast forwarded 8 months when she and her friends saved the Crystal Empire. The after party that Pinkie threw was enough to power the Crystal Heart for an eternity. The festivities were grand, but Twilight spending time with her brother and his wife was enough to make her happy. The week that followed Sombra’s defeat was difficult for Princess Cadence since she used her magic to protect the Empire by herself.
Twilight?

A voice rang into her memories. She recognized the voice immediately. It was Spike. An image of the Canterlot Castle entered her mind. Nightmare Moon was sitting on Princess Celestia’s throne with Spike standing by her side. He was dressed in an old jester’s costume. In his hands was a chest with the 5 Elements of Harmony inside.

Twilight tried to turn away from the image, but then it flashed to Applejack knocking down her own apple trees. She and so many other hypnotized ponies were destroying Sweet Apple Acres. She turned her head away, but found herself in the Crystal Empire. Rarity was there in a military uniform, tearing down the defenses of the Empire. Princess Cadence and Shining Armor had their armies ready to defend, but they were quickly washed up by Sombra’s dark magic.

“NO!”

One of the levers on the console ripped right out of the base, and the TARDIS began to spin. Alarms began to ring as everypony began screaming. All except the Doctor. He grabbed the broken lever and pulled out a silver device from the console. Twilight only got a glimpse of it. It was a silver stick with a blue light coming from the end of it. She saw him hit the underside of the lever with the light before he put it back into its empty slot. He shone the light over the spot before he threw it up. The lever was working again.

He galloped over to a large switch. “And we found it!”

The room stopped shaking. “Found what?” Twilight asked.

The Doctor pushed the final lever forward. “A weak point in Nightmare’s line of defense. We are landing on the Moon very shortly.”

Twilight’s head began to hurt. “I think I’m gonna be—”

Twilight immediately ran into the hallway. The Doctor smiled and continued monitoring the TARDIS controls. “Just gotta park right here!”
He pulled back a switch and the TARDIS stopped. The engines died down as the Doctor grabbed the monitor. “We’re here. The Lunar Ring of Maria,” he said.

Princess Luna froze. “You brought us back to where we were banished?”

“Oh no, a little farther away from there. I’ve parked her in the gardens of your castle,” he said.

Twilight returned with a bucket. “I’ve extended the atmospheric shields to encompass the whole garden. We should be fine once we get inside, am I right?”

“Yes. Once inside the castle walls, there is an atmospheric shell that had allowed myself to breath. We should be safe.”

Twilight smiled. The Doctor motioned everypony to follow him for the time being. He threw up the doors, and Twilight’s eyes couldn’t stop expanding. In front of her was a giant castle in a cave. The castle was made of marble and gold with coats of arms all over the place. The coat of arms were decorated with Luna’s Moon rising over Equestria with shooting stars surrounding it. The cave they were in was beautifully decorated with a memorial to two alicorns. Their faces could not be recognized since they were blank. One of the alicorns were definitely a male given the body structure. Upon looking at the memorial, Twilight felt her heartstrings plucking. The two looked so sad.

The princess of magic found herself stepping onto the surface of the moon. Immediately she felt the foreign history of Luna’s rage build inside her. Her anger and sadness washed over her like a wave. The castle was something to behold. “This is beautiful,” she said.

Princess Luna smiled as she approached Twilight. “We tried to outdo our sister since she had our parent’s castle. It is a remarkable treasure that we keep intact. One day, we may bring the Lunar Castle to Equestria.”

Twilight looked forward to it. The Doctor walked forward with Derpy by his side. “Well then, we can stay here for the time being. We need information on what we are dealing with.”

Twilight nodded. The history that this castle had seen may be what she was looking for. What knowledge could be behind those walls? What secrets could-

“Oh, we just forgot. Our sister sent us some of these weird cookies during my banishment. I never got to eat them. This time, I will remember to find them!”

Nevermind.

Luna Remembers

The castle’s interior reminded Twilight of Canterlot. The architecture was almost an exact replica of Canterlot, now that she thought about it. It would make sense because of how Luna was able to maneuver the elite city without difficulty. The walls were draped with beautiful tapestries with many of the constellations Twilight found incredible. She was being led by the princess of the night, and behind Twilight was the Doctor and Derpy. The pair seemed to be conversing between themselves about random things. Twilight heard some of the words they were exchanging, yet she had to block them out of her mind. There is no way anypony could’ve had tea with Starswirl.

Twilight looked up towards the ceiling. Pegasi statues with spears stood on support beams. For a single moment, Twilight had to tell herself not to look away. Mainly because she was fascinated by the beauty that went into that work, and the material used to craft it.

“Solid gold,” Luna said.

Twilight looked back to the princess. “I’m sorry?”

“The statues are made from solid gold. I found a lot of useful things on this rock during my imprisonment, some of which went into the design of the building,” she said.

Twilight nodded and looked back at the Doctor. “How do you know him? You two seem to know each other well.”

“He was there when I needed him. It started when I was banished here…

1000 years earlier…

Luna was in disbelief. For one moment, she had lost control of the powers she learned from Sombra’s magical library and the next, she was on the Moon. Her shock turned to anger as she screamed toward the planet below, alas, space was unforgiving. Her voice was confined to her Moon alone. There was no way she was ever going to reach her betraying sister. Luna collapsed on the ground and sobbed.

“Tis not fair! Tis not fair!” she screamed. “Thy heartless wretch! We are deserving of the throne before thee!”

No response came from the planet. She didn’t expect it to happen. Luna sighed as she walked away from the planet. She remembered the day it all started. While Celestia and Sombra were fighting, she had stolen into the library and ‘checked out’ a few spell books and scientific writings. In the books, there spoke of a rare phenomenon where the Moon would cover the Sun, creating darkness across the land. Luna only stole a glimpse of the spell before she fled. Her jealously toward her sister blinded her from the truth.

Luna looked up from her memories. In front of her was a large cave. She sighed as she had found her new home. She approached the cave and sat there. Being a creature who knew great forms of magic, Luna kept herself entertained by carving into the walls of her shelter. She replenished herself daily with the right nutrients to keep her health up, seeing as food was impossible on the barren rock she called home. When she figured it was night, Luna positioned herself to sleep with Equus as her night light.

As weeks and later months passed, Luna found herself completely bored out of her mind. Her usual tactics for keeping herself occupied soon bore no fruit when it came to relieving herself. Her cave wall was soon home to two great alicorns, one tall and male while the other was female. Luna didn’t know why, but she cried whenever she found herself gazing upon her work. Something was completely wrong, but she could never find herself willing to destroy it.

One day, while Luna traveled the lunar surface, a shimmering metal had caught the princess’s attention. Upon further inspection, Luna discovered a mineral she had not known to exist: gold. Seeing a chance to work, Luna continued to dig up the metal, finding other minerals in the process. The young alicorn’s mind raced and imagines a beautiful castle. Luna was not going to let Celestia live the luxurious life alone.

Over the next few months, Luna was hard at work building her new home. If she wasn’t going to rule Equestria, she was going to rule space. She commanded the stars, so she was going to reign over her sister. With the minerals inside the Moon, Luna was able to construct a castle, mainly from gold and quartz. The body of the castle was complete, but if Luna were to reign, she would need a throne, servants, and a beautiful garden in the back. Summoning Shadow Ponies, Luna put them to work. Some had descended to the planet to steal more supplies. Today, ponies remember them of being supernatural monsters.

Luna loved her subjects back home, even though they hardly credited her for her beautiful nights. While her mission was to return and show Celestia just how powerful she can be, her duty would be to her subjects. Celestia had wronged her, not the innocent ponies themselves.

With the castle complete, Luna sat proud at her new throne. Her victory was short-lived, however, as reality settled in. She was sent to prison, and she built the world’s largest and most luxurious prison cell. She wasn’t royalty, she was the Most Valuable Prisoner. She skulked around her castle, hoping something could happen. She looked down to the planet and wished to return. She tried screaming to her sister, begging her to reconsider.

300 years passed before Luna accepted her situation. She awoke from her sleep every day and explored her Moon. The mine shaft she found on her first day provided more than she expected. She found more jewels, magical artifacts, and even an underwater basin. She spent more of her time swimming and building from the jewels. The magical artifacts gave her the freedom to experiment just as Starswirl used to do. She was her own wizard.

One day, as Luna sat in her empty throne room reading an old poem she wrote, she heard a sound echoing through the halls of the castle. A whirrrrrr’ing sound it was. Luna was confused, and with confusion followed curiosity. She explored her castle once more, occasionally running through her servants. She threw up the doors leading to her balcony, and was at a loss of words. On the edge of the balcony was a blue box. A simple blue box with a light on the top. The box appeared to have doors, and before she could get close to it, they opened. Inside was a brown stallion and a pegasus. They both looked at her with curiosity. The pegasus approached her slowly.

“Doctor, is that—?”

“I believe so Derpy. It’s her.”

Luna was in shock. These ponies knew her name? She approached the two. “Um, welcome to our Moon. I be Princess Luna, and who art thou?”

The stallion was the first to speak. “I’m the Doctor, and this is Derpy Hooves. I am sorry, but we were just passing through.”

The pegasus, Derpy, looked back at the stallion. “Doctor! We just met Princess Luna during her banishment, and you want to leave already?”

“Being here is bad enough. We could very well have given Nightmare Moon a way to escape,” he said.

Luna was heartbroken. “Please, while the legends of Nightmare are true, that is not who I am today. If it pleases thee, would’st thou like a cuppa tea?”

The Doctor’s ears perked up. “Tea sounds nice. Thank you.”

The Doctor closed the door behind him and locked the door. He noticed Luna looking at him. “It’s a habit of mine. I always have to lock the door before I leave.”

Luna nodded and showed the two to her dinning room.

As it turns out, the Doctor and Derpy were there a good 5 days. The three of them shared laughs and tears as time went on without the Time Lord. Derpy was playing ‘Keepaway’ with the Shadow Ponies while the Doctor and Luna talked. When the time was up for them, Luna was beginning to feel heartbroken, but her luck changed for the better.

“Would you like to come with us?” the Doctor asked.

Princess Luna was overthrilled. She agreed and entered the Doctor’s mysterious blue box. Since Luna’s imprisonment was never recorded in the present, she was free to go anywhere but back to Equestria. As long as Nightmare Moon’s shadow stayed on the Moon, nopony would notice when the Princess of the Night disappeared.

“—and when we returned, the stars were forcing me to turn back to Nightmare Moon. The Doctor and Derpy had already left when they knew the time. They told me to hang on and never let anger consume me like last time. The next thing I know, Celestia was standing in front of me. That was the night you used the Elements.”

Twilight smiled back at the Doctor. “He was your hero.”

“Oh yes. We traveled everywhere and anywhere. Since I had no timeline on the Moon, I could return at any date in history. He brought me back on the 1000th year, and that’s when my timeline continued. We did a lot during our travels, but there are some things I would not like to remember.”

“Like what?”

The Doctor stepped in. “We were on the planet Raxcarlificus in the year 4,690, and there are strict rules when it comes to companions. See, there are no ‘friends’ on the planet, just, um, lovers.”

“Derpy and I faked marriage with the Doctor to avoid prosecution,” Luna said, hiding her face behind her hoof.

Twilight resisted laughing. “We managed to fool the government, but I discovered that I’ve never kissed a stallion before, and I ended up kissing his mane. It was humiliating.”

“You three get a fake divorce afterwards?”

The Doctor sighed. “Very funny.”

Twilight smiled and they all continued walking through the halls.

BRAINSTORM!!

The large doors flew open, exposing the ponies to the greatest library in the universe. During the 300 years of isolation, Luna had read almost every single book created during her banishment. Thanks to her Shadow Ponies, she was quite entertained with some marvelous works of art. Some of those works were made to live by Luna’s extensive research of dark magic. The characters in some of her books only lived for a short amount of time, however, but they were companionship.

Twilight’s eyes widened as she drank in the library. There were 3 stories full of books, all neatly assorted by name and decade written. In one level alone, Twilight could read a centuries worth of marvelous works. To her, history was preserved in Luna’s library.

The Doctor looked amused. “Still trying to top my library?” he asked.

“Please Doctor, this is a book store compared to yours. You have the complete works of many great unicorns in your library, but I have the most famous collection,” Luna said.

The Doctor nodded. “The Complete Works of Starswirl the Bearded are a great collection. You beat me in getting those,” he said.

Twilight spun around. “You have the Complete Works of Starswirl the Bearded?”

“All 256 volumes, including 10 out of the 12 Lost Star Scrolls. Those are extra.”

“Star Scrolls?” Twilight asked.

“Oh yes. During Discord’s reign, Starswirl the Bearded experienced Enlightenment. While details of what he experienced are fuzzy, one thing was clear: he spoke through Time. According to legend, Starswirl the Bearded claimed that he was visited by spirits of great power and wisdom. Legend has it, that he wrote whatever those spirits spoke to him and divided them all up into 12 magical tomes. They could contain anything from brand new magic to priceless information only shared by higher deities. According to legend, and my personal experience with the lunatic, all of the Scrolls must be assembled before they can be opened,” Luna said.

“The Lost Star Scrolls are Starswirl’s only great treasure. While he created many great spells and opened gateways to other dimensions, the Scrolls are the greatest of all.”

Twilight’s jaw dropped to the floor. “Right then, we need information on how we can defeat those 4 below, and with Twilight’s broken Element of Harmony, that will be difficult to find. We might as well get started,” the Doctor said.

The four ponies nodded to each other and went their separate ways. Luna carried Twilight with her all the way to the top of the library while the Doctor and Derpy stayed on the ground levels. Luna smiled at how she remembered seeing the Doctor and Derpy for the first time. She remembered how they were amazed with her library, even though half of it was still incomplete. She remembered when they both ran around and reading through her extensive collection.

As time went on, the 4 ponies found nothing to help them defeat Sombra and his allies on the planet below. Every book they found were either storybooks, autobiographies, of fact books surrounding the Elements of Harmony. With the Elements out of order, there was no way a story about a mare who lost a horseshoe will help them with anything. Twilight had no idea what to look for. The Doctor and Derpy left the library while Luna stayed behind with Twilight.

Speaking of the lavender alicorn, Twilight was perched high in the library with three books open to her. She sighed heavily as she found nothing in them. All she found were journals left behind by some of Equestria’s best authors. She replaced the books in frustration. Luna sighed as she flew up to the princess of magic.

“Still can’t find anything?” Luna asked.

Twilight sighed. “It’s like the Elements appeared out of nowhere. There is no manual into working the Elements, there is no history of the Element’s beginning, and there is nothing about what to do when an Element breaks. There is also nothing more powerful than the Elements. How are we going to defeat Sombra?”

Luna placed her hoof on Twilight’s shoulder. “Calm yourself, Princess Twilight. You’ve handled worse problems before, and I have faith you will find the answer soon,” Luna said.

“But ever since Canterlot, it seems as though my thinking has been shut off. I can’t think anymore. I think that Equestria is no longer in my hooves. I think the Doctor should save us because I have no idea how to fix this,” she said.

Luna sighed. “How many times has he saved us before?” Twilight asked.

“Oh many times Twilight. He saved us from so many evil things that even I or Celestia could no fight. Enemies who have knocked on our front door were greeted by the Doctor, and I’ve seen him do it. There are many wonderful things about the Doctor, but he is not a god. He cannot do anything all by himself. He needs help and he relies on his friends to help him. You are very much like him Twilight. You both have a problem that cannot be solved alone. It will take the both of you to save us all.”

Twilight smiled. They both flew down to the ground and followed the Doctor and Derpy to the kitchen. They entered to find the Doctor scrambling around, gathering ingredients from Luna’s cabinets. He hoisted a bag of flour on his back and ran as Derpy was busy reading a recipe book. She was wearing a chef’s hat and apron.

“Eggs?” she called out.

“They’re here!”

“Milk?”

“You’re sitting on the carton,” the Doctor said.

Derpy looked down and grabbed the milk. “And finally flour?”

“Right here!” The Doctor heaved the bag on the table.

Derpy smiled. “Yay, now I can make us all a good breakfast. I will be ready soon,” she said.

The Doctor smiled and turned to Luna and Twilight. “She has used every single ingredient in my TARDIS and now she’s hungry. I probably should’ve stocked up beforehoof,” he said.

Luna smiled. “She did make the best muffins. I miss her cooking.”

“Oi, I cooked as well when we picked you up!”

“I don’t like eating coal, Doctor,” Luna said.

The Doctor smirked. “Anyway, you girls find anything that we can use?”

Twilight shook her head. “Not a single bit of information that isn’t news. I’ve studied many different sources of the Elements and they all say nothing on how to fix them. I wish we had a clear idea what to do so we can do it,” she said.

Luna shrugged. “I released all the information that I know about the Elements. When Discord was once ruling Equestria, we found the Elements inside a chest from the wreckage of an old ship. We figured that they were from a distant land.”

Only the Doctor caught her lie. He was the one who told Luna where to look for the Elements the first time around. She was holding back something important about the Tree, but he didn’t ask any questions. If Luna hasn’t said anything to her, then he shouldn’t. “That doesn’t help us much. We can’t guess where the chest came from. It’s as if the Elements just spawned into creation,” she said.

The Doctor sighed as well. Suddenly, they heard the sound of wood falling to the floor. They all turned around to see Derpy standing there with a hoof with batter. Her wooden spoon was on the floor. Her eyes seemed to be focused in one direction. Derpy was looking at what was behind the trio: a sandy colored wolf. The wolf was looking at her with curiosity in its eyes. Derpy felt something racing inside her as she continued to stare at the wolf.

The Doctor moved forward. “Um, Derpy?”

Derpy turned to him. “The Elements are like family: they care for each other,” she said.

The three were confused at Derpy’s comment. Once she said that, she felt limp and collapsed. Luckily the Doctor was there to catch her.
Twilight looked behind her, and saw nothing. There was no wolf at the spot where Derpy was staring at.

“Derpy? Derpy?” he called out.

Derpy’s eyes opened and they were as wall-eyed as usual. “Hi Doctor! What happened?”

The Doctor chuckled. “You just slipped on some of the batter, that’s all. Lucky me I was there to catch you.”

Derpy chuckled as she sat up right. Twilight moved forward and tried staring into her eyes. “You seem like yourself, but you weren’t earlier. I
wonder what got you so upset,” she said.

“What do you mean?”

“You said something earlier. Something about the Elements being like f—”

Suddenly, Twilight’s mind exploded. A thousand thoughts raced through her mind faster than any other idea before her. Without saying another word, she bolted out of the kitchen and towards the library. The 3 baffled ponies only followed her. When Twilight entered the library, she flew up to the top of the room and grabbed 3 books. Each one was a book written by Starswirl the Bearded. She flew back and threw one of the books open.

The Doctor looked up at Twilight, and what seemed like a second later, he understood what she was thinking.

“The Elements are family!” Twilight said.

“We know Twilight, Derpy told us that,” Luna said.

“And she’s right!” Twilight shoved a book in the lunar princess’s face. “Starswirl studied the Elements while you and Celestia had them. After what took years to figure out, he came up with the ultimate theory about the Elements!”

“And that is?”

“They’re family. This is Starswirl’s hoofnote on the subject.” Twilight removed the two papers and began reading:

On the 15th day of the Cycle of Winter, I have discovered a peculiar fact about the Elements of Harmony: they are alive. These Elements are what has brought Equestria to peace numerous times already, yet I wondered how they can retain all that power they eat up. 2 nights ago, I came across the Elements ‘praying’. Their energy signatures were sky rocketing and pulsing, like the actions of a pony’s heart. This led me to experiment on these gems, and there is so much to them than I once believed. These Elements have the power to replenish themselves after every attack almost immediately as long as they are together.

The Elements are alive even as I write this hoofnote. I will continue my studies on the matter and return for a full update.

Twilight looked up. “They’re alive. The Elements of Harmony are alive!” she exclaimed.

Luna looked back at the book. “There’s another hoofnote, but it appears as though Starswirl was panicking,” she said.

Twilight looked back at the book. Indeed the writing looked rushed. Before Twilight had a chance to read it, the Doctor stole the book away. Twilight jumped as he abruptly slammed the book shut and hid it away. Luna looked at him, stunned. The Doctor didn’t say anything about the book. The princess of magic was only able to get a glance at 3 words in the hoofnote: Elements of Disaster.

Derpy sighed. “So if the Elements are alive, should we help them?”

“Yes, and we can do that. Princess Luna told me about the Discord incident a few months ago. From what I understand, Discord targeted the Elements because he knew that without them, he can cause as much chaos he can without anypony stopping him, right?”

Twilight nodded. “And if it took all 6 of you to fully restore their power, it will take 6 of you to mend the Element of Magic.”

“We can find my friends! We can repair the Elements!”

“And Discord will have a reason to worry. If we can cause an uprising in surrounding towns, like Ponyville, all their attention will be geared towards the resistance instead of us. We can find your friends and find the Elements at the same time!” The Doctor was grinning like the mad pony he was.

Luna stepped forward. “Doctor, we must have a clear idea about the location of the Elements. They could be anywhere in Equestria,” she said.

“That isn't likely. While Sombra knows that you all have been defeated, he needs to be absolutely sure that there are no more threats. If the Elements changed loyalty to any other ponies that you may've come across, then their power goes to them. Keep the Elements nearby would be a smart idea on Sombra's part,” the Doctor said.

"So we go into Canterlot Castle, steal the Elements and raise the Sun against this ruthless night?"

"Just about sums it up," the Doctor said. "We will need the Bearers though. If we can turn your friends against their corruption, then we have a shot at taking back the kingdom."

The four ponies smiled. “Right then, we’re off!”

“It’s time to take Equestria back!” Luna proclaimed.

“Oh yes! Allons-y!”

The four ponies dashed out of the library and into the gardens. The Doctor blew past the doors, and once everypony was in, released the brakes on the TARDIS console. The room began rocking back and forth at the TARDIS dematerialized from the Moon.

The welcoming committee

The control room began rocking back in forth, throwing Twilight’s stomach into every twist and knot in creation. If she lost her lunch in the TARDIS, would the Doctor forgive her? She was about to find out when Luna gave her a bucket. The bucket was her saving grace.

They had left the Moon a while ago, and with some piece of equipment that the Doctor had, they were on their way to finding one of Twilight’s friends. The Doctor amazed the princess of Friendship even more when he revealed what he was. A Time Lord? Such a name was only mentioned in myths and storybooks that pre-date Celestia’s Reign. A race of beings who had a near unlimited supply of knowledge and power, and with a civilization that lasted billions of years. The name ‘Doctor’ was never mentioned in any of the books she read about this race, but if he was in it, he would be everywhere. He talked quite a bit about his race before, but Twilight noticed that once he was done talking about them, he would stare into nothing like he was sad.

The Doctor pulled on the brakes. “We are back in Equestria,” he said.

Luna smiled. “And they don’t know?”

“No. I had the engines on silent and have her in camouflage mode. We cannot be detected by any sort of magic. I guess that would’ve helped us get past the Shadow Ponies earlier, but where’s the fun in that?”

Twilight face-hoofed. The Doctor better be smarter than he is letting on. Her eyes scanned the control panel in front of her. Somehow, this disorganized series of panels provided the best way of navigating between the Moon and Equestria. On the control panel next to the Doctor was the book he snatched from her back in Luna’s library. A hoofnote left by Starswirl was somehow forbidden to her. It was like he and the Doctor know something that shouldn’t be shared. A secret concerning the Elements.

The Doctor stretched his neck. “Come along Ditzy, we need to find your friend. Rainbow Dash, right?”

Ditzy nodded. “Okay, I got a trace of her in the Everfree, and with what you all said about that place, I have a reason to believe that she may be in danger. We find her before anything else does,” the Doctor said.

“Our friend Zecora lives here. Maybe she can help us,” Twilight said.

“The zebra from Nightmare Night several months ago?” Luna asked.

Twilight nodded. “We remember that night perfectly.”

The princess of magic chuckled nervously. She wanted to forget that night. “Where does your friend live?”

“In the center of the forest. There is a grove of Poison Joke not far from her hut. Let’s find Rainbow first.”

The Doctor opened the doors. They landed in a clearing somewhere in the forest. Everything would’ve been fine, but since Nightmare defeated Celestia, the Moon was high in the air, and it appeared to not have moved at all since their escape. “This place hasn’t changed since I last saw Starswirl,” the Doctor said.

Twilight scoffed. “You cannot have met Starswirl. Time travel may be possible, but I can only go back about a week,” Twilight said.

“Well I have, and we even went exploring around here. We went down that bog once and found a basilisk. Sucker was huge.”

“I remember that basilisk! Celestia and I would throw stones at it whenever it got close to the castle,” Luna said.

“Yeah, I remember it saying that all you had to do was ask it to go somewhere else. It was tired of the stones.”

“It was a nice time seeing Starswirl,” Ditzy said.

The Doctor smiled. “I can understand you remembering him Luna, but you Doctor? I can’t see you and Starswirl talking,” Twilight said.

“We do more than talk. Ditzy often trades recipes with him while I battle at chess,” the Doctor. “He cheats.”

“His muffins were amazing. Too bad I lost the recipe.”

The Doctor placed a hoof on Ditzy’s shoulder. “I have it memorized. We can write it down later so you have a copy.”

“Yay!”

Suddenly, there was a loud crunch. The four ponies stopped in their tracks. They were in a thick brush. Twilight and Luna stood ready to defend. The Doctor and Ditzy were still. “What was that?” Ditzy asked.

“Perhaps somepony is following us?" Luna wondered.

Twilight shook her head. "Must be a big pony."

A loud roar blasted through the forest, hitting the four. Twilight knew that roar very well. Too well. Before she had time to speak, the trees surrounding her came crashing down. From beyond the bushes, the Timberwolves leaped out. Ditzy and Twilight screamed while Luna charged her horn. She fired a magic blast, scattering the branches of the Timberwolf. Four more began running at them from behind. Without a second thought, the four ran. They jumped out of the brush and into a clearing.

Twilight looked behind her. The Timberwolves were getting closer. She fired a magic blast, but missed the leading Timberwolf. She turned and continued running. She noticed the Doctor was trying to run on three hooves as he was fidgeting with a silver stick. The stick had a blue tip on the end. He growled and cursed about not having hands. Twilight understood that term.

“What is that?” Twilight asked.

“It’s a screwdriver,” he responded.

“That is not a screwdriver. That looks like a tiny flashlight.”

The Doctor chuckled. “Looks can be deceiving, can they? Ugh, Ditzy, you have open hooves, can you switch it to Setting 496?”

Ditzy nodded and flew up in the air with the screwdriver. “What, are you going to build a cabinet to throw at them?”

“No! Setting 496 is Molecular Depression. By releasing a sonic wave at the ground beneath the Timberwolves, I can cause the ground to weaken and depress beneath them, creating a hole. Have you got it yet?”

Ditzy fumbled with the device. “Got it!”

“Good, now press the button, and—”

Ditzy pressed the button, but she didn’t aim. The sonic wave was aimed at the hooves of her friends. The ground beneath them weakened and all three fell down the hole. “Ditzy!!”

The pegasus blushed. “Whoops, my bad.” She readjusted the device, and pressed the button. This time, the ground underneath the
Timberwolves collapsed, sending them all into the ground. Ditzy looked over and dropped the device into the Doctor’s hooves.

“Ok, that should take care of everything for a little while. Ditzy, a little help?”

The pegasus flew down to help the Doctor. Meanwhile, Luna had to carry Twilight due to her injured wings. She never realized how much she relied on them until she was injured. She felt like a regular unicorn again. The four touched hooves onto the ground and turned to survey Ditzy’s work. She was still blushing from her mistake, but the Doctor didn’t mind. “What is that thing?”

“A Sonic Screwdriver. Think of it as a little bit of the TARDIS. My most faithful of gadgets that have well over an infinite amount of applications,” the Doctor said. “I love this thing.”

“Don’t let my sister in law hear you say that,” Twilight said.

Luna chuckled upon remembering Cadence’s Art of Shipping chart she had lying around the castle. “Right now, we need to focus on finding your friends. Where is this Rainbow Dash?”

Upon saying the pegasus’s name, a loud roar echoed through the forest. The Timberwolves had returned, but they carried an aura of dark magic. Luna tried firing a spell at them, however it deflected off its chest and flew into the forest. The princess of the night gulped. Without another word, the four high-tailed it into the forest. Behind them, the Timberwolves howled before commencing the chase. The Doctor tossed up the Sonic Screwdriver to Ditzy. With Setting 496 already programmed, the wall-eyed pegasus began firing. Unfortunately for the 4, the Timberwolves were smarter than the others. They leaped out from the holes the second they fell in. They were even smart enough to evade the traps altogether.

Luna led the group around a sharp corner, and kicked a boulder into the path of the Timberwolves. The boulder was smashed into dust instead of breaking the Timberwolf structure. The four continued to run, but found themselves at a dead-end. In front of them was a cliff, and with two ponies who couldn’t fly, the chances of escape seemed to be slipping away. The turned back to face the Timberwolves.

The predators stopped, completely sealing their lunch in. They slowly approached the four, and before death could great them, one of the Timberwolves exploded in a green dust. The last thing they all heard was a small yelp from it. The four looked around, and noticed a pegasus in the trees with saddlebags filled with bottles. Twilight couldn’t make out what was in them, but she guess that they were potions. The Timberwolves growled at the pony.

“You want to hurt my friends, you’re going to have to get through me you pile of firewood!” yelled the pony.

Instantly Twilight knew who it was. The pegasus leaped into the air and threw some more bottles at the Timberwolves. Two exploded while another opened its jaw to swallow it. The potion exploded, but did nothing to the wolf. The pegasus got into the Timberwolf’s face, kicked it with its hind legs, and flew off. The Timberwolf quickly followed the pegasus. A few minutes passed by before they heard a yelp and a crash.
The crash seemed to have been made by a falling tree.

Silence filled the forest. The ponies stared into the thick brush, expecting something to happen. Indeed something did. From out of the darkness of the Everfree Forest, a pegasus came flying at them. She seemed to be carrying something in her hooves. The pegasus came into full view and dropped whatever was in her hooves. A pile of wood. Twilight smiled. “Poison Joke?”

“I guess there are good things that come out of being an egghead,” Rainbow Dash said. Without another word, the cyan pegasus tackled Twilight. The princess yelped in pain as her friend trapped her in a bear hug. “We thought you were dead!”

Twilight sighed as she wrapped her hooves around her friend. “You’re not getting rid of me that easily, Dash.”

Author's Note

I will try to pump out two chapters one a more regular basis and get back to what I promised you. I am transferring this story from fanfiction.net so this is my actual story. I am adding one new chapter though once the story itself is done so watch out for that. Flutter On!

Zecora and Rainbow Dash

The 5 ponies began walking through the forest. Twilight and Rainbow led the group through the dense forest. Twilight told Rainbow all about what had happened after she woke up, including being sent to the Moon, reading Starswirl’s own hoofnotes, the TARDIS, and pretty much everything else in between. She also told her about her handicap of not being able to fly. Rainbow sighed as they continued walking. “I guess I’m going to have to teach you how to fly again, huh?”

Twilight nodded. “I guess so, and I was getting good at it. So what’s happened since we last saw each other?”

Rainbow stopped midflight. “Everything went wrong back in Canterlot. Sombra sent Pinkie and Fluttershy to the dungeons with Princess Celestia. She didn’t look so good with her broken horn and Pinkie had not said a word. Her mane went flat as they carried her away. I couldn’t stop them with my wings. They got rid of me before I had a chance to escape. I was plopped out here in the middle of the forest, and I thought I was going to die, but Zecora found me. She lifted the curse off my wings and I’ve been here ever since. It’s been tough out here, especially with the Forest retaliating.”

“What do you mean?”

“Zecora said that for a while, the Everfree Forest started fighting. She’s seen plants move and the mist from within get thicker. She says something is coming.”

Twilight pondered that for a moment. She knew the Everfree was untamable and free when it came to the weather. “How long have you been here?” the Doctor asked.

Rainbow looked over. “Who are you?”

“I’m the Doctor,” he said.

Rainbow raised an eyebrow. “Doctor who?”

“Just ‘the Doctor’. I helped nurse Twilight back to health, but it was Luna who saved her,” he said. “And I’m sure you know my faithful assistant, Ditzy.”

Ditzy looked over at Rainbow. They touched hooved and laughed. “So this is where you fly off to after your mail runs: off with your coltfriend.”

Ditzy’s face turned bright red. “He’s not my coltfriend. We’re just friends that’s all,” she said.

“Uh huh, sure and Twilight didn’t have a small crush on that guard in the Crystal Empire.”

“Can we stop talking about Flash already? He is just a version of a guy I met while in the other world, that’s all he is to me. There was no crushing and no flirting so quit it!” Twilight barked.

Rainbow laughed. “Oh c’mon Twi, you know I’m pulling your tail.”

The lavender alicorn rolled her eyes. “Sure, and the Doctor is a Wonderbolt.”

The Time Lord smiled. “I actually am a certified Wonderbolt in one of my earlier lives actually. General Firefly and I were really close friends for an awfully long time and still are,” he said. “He has a bit of a drinking problem though, and I take responsibility for that.”

Rainbow looked over. “General who-now?”

The Doctor waved it off. Rainbow shrugged and continued flying next to her friend. “Seriously though, you do have a crush on the guy.”

Twilight made a move to grab Rainbow Dash, but she only elevated a few more feet off the ground. She scowled at the pegasus. “Show some interest with a male for half a second and I never hear the end of it. First Rarity tries to set me up with him and now he is being used against me. Brilliant,” she muttered.

Rainbow laughed as she finally touched ground. The ponies continued walking through the forest, eventually finding the hut of Zecora the Zebra. Rainbow knocked a few times on the door before entering. Everything on the shelves looked exactly the same as the last time Twilight was here. The creepy masks that followed her every step were still hung from the ceiling as a security system. That is probably one reason why nopony tries to enter without her permission. Those masks probably can speak.

Bottles of variously colored liquids lined the shelves. Potions that ranged from simple healing spells to complex incendiary spells and Transfiguration. Rainbow flew up and replaced whatever leftover potions she had in her bag. Twilight had the displeasure of trying a Transfiguration potion once. She often wondered the life of a dog, and when she got it, she was happy to be a unicorn again. It was one experience where she and Spike knew what they were talking about.

In the middle of the room, right next to a giant cauldron of a green liquid, stood the zebra herself. She was muttering an incantation in her native tongue, but when Rainbow landed on the floor, she stopped and turned. She looked weary like she was working non-stop since the invasion.

“Please Rainbow Dash, if you will come in, please be as silent as a falling pin,” she said.

“Hehe, sorry Zecora, but I found Twilight and some new friends of hers.”

Zecora turned to greet the new friends of Twilight, but when her eyes rested on the Doctor’s, she smiled. “My eyes deceive, it is the Doctor. So long have I waited to enter my front door,” she said.

The zebra inched closer to the Time Lord and grazed his muzzle. “You’ve seen me before?”

“And I fear we will meet some more. Please sit and you will see, there is much to fear in this monstrosity.”

The ponies all glanced at each other before approaching the cauldron. The liquid bubbled from the flame, and before Twilight knew it, an image popped up inside the liquid. She recognized it immediately as the Crystal Empire. From her last vision, Sombra was near victorious against Cadence. The Empire looked dark and sad. The Crystal Ponies were all chained up and forced to and from the mines. The palace was surrounded by living shadows and Changelings.

Twilight focused more into the image. Underneath the palace was the podium for the Crystal Heart, but something about it was different. It wasn’t spinning like it used to. Instead, the Heart was motionless and dark, like all of the happiness and love that was inside was suddenly gone. The surface was cracked like a broken heart is normally depicted.

“Dear Celestia, he won,” Rainbow said.

“I’ve seen something like this before. He may have won, but the war isn’t over yet. They still don’t have it,” the Doctor said.

“Have what?” Twilight asked.

Ditzy and the Doctor exchanged looks. They knew about the artifact she would later find. The Tree and the power within. Twilight looked closer into the image, and noticed a familiar pony standing beside the Heart. A unicorn with purple curls in her mane and a crystalized military uniform. It was Rarity guarding the Heart. Her eyes still green from the dark magic used against her.

“Rarity.”

Zecora nodded. “Dark in mind as her heart, setting her free will play a major part.”

Twilight nodded. “What can we do?”

Zecora put a hoof under her chin. “The answer be a holy key, so where is your Element of Harmony?”

She hung her head. “Broken, but I think we can make it right. We need the Elements to restore it,” she said.

Zecora nodded. “That be done is the easy path, but what happens now against the dark’s wrath?”

“Well, we need to cause a revolution. Something to keep Sombra and his goons distracted, but what can we do?”

“Better not to flee, you may need the Harmony—”

“Free. Harmony free,” the Doctor interrupted. “We must free the agents of Harmony, meaning your friends.”

Zecora glared at the Doctor. “Perhaps another to please your aching heart, but be warned it is one difficult part. A dark lord’s death is the key, to rid us all of the Unholy Trinity.”

That last line directed to the Doctor. “But, there’s 4 of them,” Ditzy said.

The zebra looked over. “I know what I said and I said what I meant, now it’s time to sleep your day is well spent.”

At that point, Twilight yawned as did everypony else. Zecora motioned to a section of her hut that was draped in a large brown cloth. Twilight opened the curtain and two hammocks were in place, one on top of the other. Twilight took the one below while Derpy took the top. Princess Luna looked around and found a spot where she could rest.

Within seconds, all but Twilight were sound asleep. From beyond her fight to sleep, Twilight seemed to overhear an argument between Zecora and the Doctor.

“Interrupt me and make false words, surely your mind has gone to the birds!”

“I know a lot about your magic in potions, including prophecy, but the tree cannot be known. It isn’t time.”

“’Time is not the boss’ are those your words, or have you lied you ungrateful curd?!”

“I need this timeline to progress as slowly as it can. We can win, but without ancient magic. Without the tree.”

“Very well Time Lord I will remember, but now is your time to slumber?”

“Not yet. I’m not ready. Are you sure about ‘A dark lord’s death’?”

Silence. The sound of hooves exiting the hut were all that were left Probably going to get his box, Twilight thought to herself. Twilight fell asleep with a tree in her mind. Tomorrow, the revolution begins.

Sombra and Discord

Sombra levitated a crystal to his mouth. With a snap of his jaw, he took a big bite out of it. The taste of crystals, normally reserved for dragons and crazy ponies, felt blissful to the dictator. With the Crystal Empire back under his control, he felt like he could kick his hooves up and finally feel like a king. That included working his subjects to the point of death. He sat in his throne and expanded his mind thanks to the dark magic. He saw his ponies working underground, making him richer by the second.

That was the fantasy.

As he ate his crystal and watched his subjects work, the rest of the Crystal Empire walked and breathed dark magic. Shadow Ponies stood guard outside his castle, ready to defend should there be a reason to do so. The pony he acquired in his successful takeover of Canterlot was busy conducting her patrols of the castle interior. His financial advisor stood by his side with a scroll in front of him. As he read the daily report, Sombra tried his best to think above the pony’s voice. He hated the daily report. If taping somepony’s mouth shut and setting it on fire were looked upon as good, he would be doing that to anypony who talked to him.

“-5 million bits in value in the one hour alone, leading to a combined total of 35 million bits of jewels during this cycle. Congratulations, Your Majesty, you are the richest stallion in Equestria,” the pony finished.

Sombra sighed. “These crystals are not to be sold to Nightmare Moon! These are all my jewels and my crystals, not hers! I make one deal with a trickster and I end up losing more than I hoped to gain! When am I going to get what’s mine?!”

The pony didn’t dare answer. “Leave!”

The pony dropped the scroll and ran out of the throne room. Sombra threw his half-eaten crystal at his advisor, but ended up hitting the door as it slammed shut. He sighed as he pulled out another crystal and began eating. “Stupid equines.”

One of the guards spoke up. “With all due respect sir, you—”

“Finish that sentence and you will spend the rest of your days as a chew toy for Cerberus,” Sombra threatened.

He shut up immediately. “I want this cycle to feel good to me. Let’s take a piece of the Griffon Territories. Which territory is available for us to capture?”

Another guard approached Sombra with a map. He unraveled it, showing the Crystal Empire, the Frozen North, and somewhere in the West, the Griffon Kingdoms. Sombra sighed. The Griffons were once very much closer to them the last time he looked upon the map. “Their wing power is great, but have no magical defenses, correct?”

“Yes sir!”

“We cannot fly unless we have heavy armor, and that can be made using the crystals, correct?”

“Yes sir!”

Sombra studied the map. “We move on the coast, running along the North. The Griffon Kingdom will have impenetrable defenses, but that can be easily taken down by dark magic. While we are there, we can probably just take the Griffons as a whole. Contact Nightmare and Chrysalis and get them to send troops up here.”

The guard looked uneasy. “If I may add, sir, that is impossible. Chrysalis is taking the dragons in the South and Nightmare is handling a rebellion that started in Ponyville. We are stretched sir. With the constant weather storms in the North, Shadow Ponies would find it hard to keep their form, and Changelings would not be able to fly. A naval invasion would be best,” he said.

Sombra looked over. “Were you a military officer before?”

“Yes sir!”

“Well then, how about this: I send you out there with a spear and a target painted on your back. If the cold doesn’t get you, the griffons will.”

The guard gulped. “Next time you object to my master plan, I will not give you a fair warning. Contact Nightmare and Chrysalis before I have you obliterated!”

The guard yelped and ran out the door. He managed to trip as he did so. Sombra sighed. There was nopony that served him more than Rarity, and he hypnotized her to be his general. At that moment, the guard came running back and threw open the doors with great force. Sombra spit out a piece of the crystal. “Your Majesty! A strange object is flying towards the Empire.”

“That is not a nice way of describing Nightmare,” Sombra said with a slight chuckle.

The guard stopped. “No sir, um, the object appears to be in the shape of a box, sir! A big and blue box.”

Sombra’s ears perked up. “What? Show me!”

The guard levitated a pair of binoculars towards the king. He looked out the window and saw the object. It was blue and it was headed their way. He grumbled to himself. “It’s probably Discord playing a game with us.”

At that moment, a loud BANG! echoed through the castle. Sombra turned around to see Discord in a weird looking hat. It looked like Pinkie Pie’s head. Of course it really wasn’t, but the god of Chaos was wearing a hat inspired by an annoying baker. He was laughing, oblivious to what had happened.

“—and I said ‘Oatmeal? Are you crazy?!’ and—”

He stopped midsentence as he realized where he was. He looked down on Sombra, and he quickly shook his hat off. He was blushing while Sombra didn’t even crack a smile. “I’m going to pretend I have no idea what you were doing and just get down to the point: what is that thing headed over here?”

“Is Nightmare visiting?”

“Focus!”

Discord gave him a blank look. “Seriously? You are asking me, a lord of Chaos, to focus on something? It’s like you don’t know me at all.”

“DISCORD!”

The god of Chaos sighed as he conjured a pair of binoculars. He peered out of the window and chuckled. “That’s nothing more than a simple weather balloon. Haven’t you heard of the Balloon Colt that caught Equestria’s eye a few ye—”

Sombra’s neutral expression said it all. Discord chuckled. “Ugh, nevermind. It’s probably a piece of junk I accidentally conjured up and it left my watch. I’ll put it away.”

With a snap of his claws, Discord vanquished the box. Immediately after it disappeared, it reappeared in the sky. This caught Discord’s attention and he tried snapping his claws again. Again it disappeared and reappeared within a second. He clapped and stomped the ground, trying to vanquish the box, but he had no luck.

He sighed. “This usually works,” he said.

Sombra roared in anger. “If you need something done right, do it yourself. Move out of the way!”

Sombra smashed the glass with his hoof and charged up his magic. He fired a beam of dark energy at the box and held it in a tractor beam. He smiled and laughed at Discord for struggling with something so easy. He fixed his attention back onto the box he held onto, but it was gone. Sombra let up his dark magic and stared at the point where the box was last located.

“Umm, what just happened?”

“Well performance issues, it happens a lot. 1 out of 5—”

“Shut up Discord,” Sombra said.

The draconiquus chuckled. “Well, it seems as though neither of our magic can hold the box, so I think it’s just some sort of illusion. There is no way that anything on this planet can withstand that mag—”

The castle rumbled above their heads. The box was flying up the castle, passing the two rulers. A strange wheezing sound seemed to be emitting from the box itself. Discord had gotten a better look at it. It was a blue tall box with two doors in the front. There was a small light on the top of the box with a sign on it. He didn’t catch the sign because it was moving too fast. That wasn’t the only thing that caught his attention, however.

As the box passed him, he noticed the wheezing sound as it flew. He had heard that sound before. He dove into his memories and latched onto where he heard that sound before.

1000 years ago…

Discord laughed as he viewed the world below him. He had turned the desert into dessert and the Unicorn Range into the world’s largest taco. He had made the clouds rain chocolate milk and volcanoes spew rainbows in the Bad Lands. He laughed as ponies tried running from whatever the hell was going on. He fixed himself a glass of chocolate milk and drank the glass itself. He couldn’t stop laughing as one pony yelped before turning into a tree.

As he looked around his new world, he noticed the Castle of the Two Sisters remained untouched. He wondered why it had survived his chaotic meltdown. He teleported into the castle and transformed into a unicorn guard. As he did so, a guard turned the corner. Discord yelped mid-transformation, but blowing a green dust in the pony’s eyes forced him into a quick nap. Once the draconiquus was fully transformed, he hoisted the real guard and hid him behind a statue. He fixed his fake helmet and began to wander the halls.

It took a few minutes, but he had found the throne room. He leaned his ear against the door, hoping to gather some juicy information about what they were planning, or better: the secrets of the Alicorn castle left behind. Discord wasn’t a fool, he knew the Two Sisters didn’t build it.
Celestia and Luna were arguing about what to do with Discord. Luna wanted to vaporize him, but Celestia thought about trapping him. Both were impossible in the draconiquus’ eyes, but he continued listening. Luna appeared to be convincing her sister on what they had to do, and before he made his escape, he heard Celestia gasp.

“He’s here!”

“Already? How did he—?”

“I do not know, dear sister, but we are ready.”

Discord froze. He expected the sisters to break the doors down, but he heard something else. A wheezing sound seemed to be emitting from inside the throne room. He continued listening and he noticed that the wheezing was getting louder, like something was approaching. The sound reached its peak before it quickly became silent.

He heard a wooden door open, which was strange to the disguised Lord of Chaos. Celestia was the first to speak. “My doctor, why have you come?”

“I found what you need to defeat Discord. Well, Starswirl and I did. We found this map in a chest on the shore of Equestria. Here, let it guide you to where you need to go,” a stallion said.

There was a short pause, followed by Luna’s voice. “We do not understand, this map is hundreds, maybe thousands of years old. How can it be—”

“Listen, you have to trust me on this. Follow the map and you will find them. Perhaps the legends are true and you can finally bring peace to this war-stricken world.” Some silence followed the statement, confusing the draconiquus. “Remember the order? I don’t exist.”

“We have not be born yesterday, dear doctor. We know your code of silence.”

Some chuckling was heard. “Good luck. Hopefully we will not meet again.”

“Knowing you, we will.”

Discord heard the wooden doors open and close. The wheezing sound began to grow again, and before Discord could storm in and find the stallion, there was silence. “Sister, can we trust him?”

“He has helped us in the past, and I believe in him today. This is a lead on where they are!”

“If they are here, then we can win?”

“Maybe. Come, we must prepare.”

Discord took that as his sign to get out. At the time, he thought he was just hearing things. He had no idea the subject in question would turn out to be the Elements of Harmony and he didn’t expect his defeat later that afternoon.

Discord was staring into space. His eyes were twitching as the memory unfolded. Sombra was confused. “Umm, hello?”

The draconiquus turned to Sombra. “I just realized I left the stove on at home. I really do need to go,” he lied.

Sombra was confused. Little did they know the TARDIS had materialized with its cloaking shields up. Twilight snuck out and magically tied Sombra’s tail with Discord’s. She quietly giggled to herself before returning to the control room. She silently closed the doors behind her and ran up to the Doctor.

Rainbow Dash and Zecora were both inside the TARDIS, and their mouths were still hanging. Bigger on the inside seemed impossible, and it wasn’t until now that Rainbow realized that Twilight’s house at the Golden Oaks library seemed to be bigger on the inside. While she did have a large library, her loft, bathroom, kitchen, and living space made the treehouse seem smaller on the outside. She decided not to think about it too much and tried understanding the concept of an old police box with an inside that could fit all of Ponyville.

The Doctor turned on his monitor and set it to ‘Home Theater’. A large screen appeared from behind the Doctor with a live picture of outside the TARDIS.

“You don’t understand, I have a rogue blue box flying around that can be trouble. Why are you suddenly scared of it? What, did it destroy your life?!”

Discord gave Sombra a dark look. “You have no idea. Anyway, I need to see Nightmare. I do believe I owe her a reason why I vanished in the middle of a good joke. The box is in the Crystal Empire, so it is your problem. Now, if you excuse me.”

Discord vanished. Sombra felt something pulling his tail, and before he had time to think, he vanished too. Everyone inside the TARDIS started laughing as they rewinded Sombra’s face as he disappeared. To the Doctor, it reminded him of a cartoon he caught himself watching judging by Sombra's face. The Doctor froze the video at the moment Sombra was teleported. Rainbow and Twilight were in tears while Derpy, Luna and Zecora were rolling on the floor.

The Doctor calmed down. “Ok, that should buy us a few minutes. Let’s find Rarity.”

Rarity

Shining Armor felt guilty and distraught. With Sombra’s return to the Crystal Empire, he led the front lines against his invading forces. He and his brave soldiers fought hard and through the front lines, and he was close to claiming victory against the Frightful Four (Sombra, Discord, Nightmare, and Chrysalis) before things turned south.

Shining had defeated the first wave of changelings and Shadow Ponies when everything went south. It appeared as though it was going to be easy to hold them off, but he was sorely mistaken. Before he could rest, however, Rarity stood up and faced him. Feeling like his hooves were glued to the snow and his magic depleted, Shining was quickly overpowered by her dark magic. With his lines shrinking, Cadence’s Royal armies began to hold the borders, but Sombra was too powerful. Within a moment, Cadence was beaten.

As the Moon rose over the land, Sombra’s dark forces gained more power and wiped out any threat of rebellion. By Sombra’s orders, the entirety of the Crystal Empire was placed on a magical lockdown while his subjects were forced back into slavery.

With the royal couple defeated, Sombra was elated to share the news of Canterlot’s fall. “Celestia crumbled like the little filly she is,” he said.

“My sister and her friends will stop you!” Shining shouted at the tyrant.

“Princess Twilight Sparkle? Oh yes, she came very close, but much like herself, the chances of victory flew out the window!” Sombra laughed hysterically. “Sorry, but no Elements of Harmony will save you now!”

Shining began tearing up and tried telling himself that what he said wasn’t true. Sombra only laughed harder, confirming his fear. The world grew silent as Shining let out a heart-breaking scream. Cadence’s heart shattered as they were both locked up. They both did nothing to fight and were both thrown into the dungeon under the city. With only his wife in the prison, the prince of the Crystal Empire began to sob.

Cadence, on the other hoof, said nothing. She didn’t know what to say. Her sister-in-law was dead. With no power to fuel the Crystal Heart, the Empire fell almost overnight, and she had to watch as her subjects lost faith in the monarchy. Sombra opened the mines and forced his subjects into slavery just how he had done before. The ponies who were able to pay Sombra’s taxes were spared from the horrible work, but received harsh responses from their fellow citizens.

As Sombra laughed at the misery of the Crystal Empire, Shining shed some tears as he quietly mourned his sister’s death. Cadence picked up a rock and began carving into the wall of her cell. Occasionally, she would slam the rock into the wall, reducing it to dust. Shining looked over at his wife and held her as she picked another rock up. She wasn’t angry, she was just too sad.

“What can we do now?” Cadence asked.

Shining looked up at the cell. “Wait until somepony stops Sombra. Somepony has to have the strength to fight him,” he said.

“But if Celestia and Twilight fell, then who—”

Cadence looked over at her husband. “Princess Luna!”

Shining nodded. “Maybe she can fight Sombra and free us. At least we need to Crystal Empire to be freed before we have the upper hoof,” Cadence said. “She is the entity of the Night, she should have the advantage in this situation.”

She knew Luna was tough, despite her recent return to Equestria. Luna was the princess of the Night, and her powers were something that couldn't be matched. She dropped the rock and lost herself in her husband’s embrace. “You know, Shining, there has been something I’ve wanted to talk to you about.”

Shining’s heartbeat began speeding up. “Oh, like what?”

“Well, you know we’ve been married for a year, and our anniversary is coming up in a few weeks, and I was thinking that maybe we should start looking toward the future for us and the kingdom,” she said.

“What are you saying?”

Cadence fidgeted. She tried asking Celestia what to say to Shining concerning this sensitive topic, and the wisdom she received was grand.

“No subtle hints, no stallion is good at understanding hints. Drop it on him if you want him to get it,” Celestia said.

“Uh, I was thinking that now would be a good time to introduce a new member of the family to this world,” Cadence said. “Maybe a little filly.”

The gears in Shining’s head turned, but nothing was happening. “I don’t understand.”

Cadence mentally face-hoofed. So much for that, she thought to herself. “Forget it.”

Shining smiled. Cadence sighed as she felt her eyelids grew heavy. Before she could drift into a peaceful sleep, a weird sound began emitting from the room. “Shining, what are you doing?”

“I’m not doing anything.”

Cadence opened her eyes. The sound was growing louder and appeared to be close. She looked around for the source of the noise, but there
was nothing in the room with them. The one guard that was assigned to them was outside the prison doors, but aside from them, there was nothing. The sound was odd. It sounded like something was wheezing like they inhaled smoke or something.

The couple continued searching, but Cadence finally found it. In the middle of the room, a large box began appearing out of thin air. Shining had to rub his eyes to make sure he wasn’t seeing things. His eyes were serving him right. A large, blue box was appearing. The box was a panel of windows and a set of large doors on the front. There was a small light bulb attached onto the top of the box. When the box had fully materialized, there was a loud bang. Both Cadence and Shining were stunned.

The doors opened, and a brown earth pony walked out with a long, brown coat. He had a messy mane with a silver stick in it. Cadence wondered how this pony liked going around looking like a crazy homeless stallion. The earth pony looked at the couple and smiled. He turned back to his box. “Yup, this is the right cell. Princess Cadence and Prince Shining Armor right?”

“That is them!” they heard Luna’s voice from within.

Cadence lit up. “Luna! Is that you? Where are you?”

Luna stepped out of the box. “Right here. Oh wow Cadence, how is it being trapped in the same cell as your husband? Have you two been behaving?"

Cadence smirked while Shining blushed. “Very funny Luna,” she toyed.

Luna smiled. “Anyway, we are here to bust you out!”

Shining Armor banged his head on the wall. “Great, I think the guard heard you, if he didn’t hear your box first,” he said.

Luna realized her mistake and shrunk down in embarrassment. “Whoops.”

The stallion shrugged. “Ok, standard bolt door with mechanical tumbler inside the door.” He reached for the silver stick. “Setting 46B should do the trick here.”

Cadence chuckled. “Excuse me, but that’s a stick, it can’t open a door. You need a key.”

The stallion looked up at the princess. “Hairpins and needles can open locks too. Have faith in my screwdriver.”

“You’re what?”

Instead of answering, the stallion aimed the silver stick at the door. With a light buzzing sound, the door lock clicked. Cadence was taken back at the magic she had witnessed, and with a simple push on the door, it flew open.

“This is a Sonic Screwdriver. Opens anything, tricks anything, and does everything else, except wood. Maybe some hairdryers too, but I’m getting that fixed. I’m the Doctor by the way,” he said as he stretched his hoof at Shining.

Shining shook his hoof. “Nice name. ‘The Doctor’! Maybe I should be called ‘The Prince’,” Shining said.

“Please don’t,” Cadence said.

Shining smirked at his wife. The Doctor approached Cadence with a hoof extended. “Nice to see you again, Princess Cadence.”

Cadence was taken back. “Again? So we’ve met before?”

“Long story, trust me. C’mon, we gotta get out of here, and quickly. Sombra’s guards will be here any minute,” the Doctor said.

The royal couple nodded in agreement, and before they could make a move to the box, a magical energy burst hit the door. The four ponies turned to see the guards standing at the doorway. The guards were not hypnotized ponies like what Chrysalis was accustomed to, but more like walking shadows. Their black armor had etchings of ancient runes that Princess Luna recognized as defensive magic, enhancing their armor. Their bodies were wispy black smoke with devilish red eyes.

Taking the front line was Rarity herself. She was wearing her crystal military uniform with matching helmet. Her eyes were still glowing green from the dark magic running through her veins. “Trying to escape is not permitted in master Sombra’s Empire. You will return to your cells now!” Rarity commanded.

Cadence and Shining held their ground. “You’re not defeating us this time, Generous One!” Cadence said. “I don’t care if you were Twilight’s friend, you are going down!”

Rarity smirked. “I guess you will be seeing Twilight again very soon, dear princess.” Without another warning, she fired a blast of dark energy.

Before Cadence could raise up a shield, the doors swung open, deflecting the blast straight back at the unicorn. Rarity dodged it with ease, but the guard behind her did not. The shadow screamed as it evaporated into nothing. The door closed, and out from the box, the princess of Friendship stepped out without her bandages around her head and wings. Cadence and Shining Armor looked shocked and relieved. Twilight was alive!

“That’s enough Rarity!” Twilight commanded.

The guards lowered their spears, but Rarity called them off. “It seems as though the new wings actually give you some form of immortality after all. Twilight Sparkle, the first unicorn to successfully control dark magic and its seductive properties. Care for a rematch?”

“Trust me, it won’t take long for you to submit. Rarity, please, you need to snap out of it.”

“Rarity is dead! I reign supreme, and once my masters fall, all of Equestria will belong to me! Guards, kill them!”

The guards charged at the ponies. Twilight summoned a magic circle from her vast collection of Starswirl’s magic spells and fired several stunning spells at the guards. Most of them fell immediately to the ground while turning others into explosive flower pots. Only a few were left still charging.

The Doctor raised his Sonic Screwdriver, and pointed it at the ground. Immediately the stones began moving up and down like the floor was a waterbed. The guards lost their balance and fell over in full armor. Their helmets knocking them out cold.

Rarity roared as she summoned Shadow Ponies to the room. A legion of 50 raised up and quickly surrounded the ponies and the box. Rarity thought she had trapped Twilight and her friends, but as the walls of the Shadow Pony’s magic began to darken, a bright light was seen emitting from within the vortex. The Shadows began shrieking and immediately exploded. Cadence and Shining Armor had created a bright light from their magic, destroying all hopes of more Shadows forming.

Rarity had enough of her minions failing. She fired another spell at Twilight, but she quickly deflected it. The energy flew up into the ceiling, spooking an off duty guard. Rarity continued to fire spells at Twilight, but since she read most of Starswirl’s notes on advanced combat spells, she was able to break down every single attack and easily deflect them. The attacking unicorn began growing impatient with her adversary and threw 3 quick spells, but not at Twilight.

The princess of Magic followed the magical bolts, and saw where they were going to hit: Cadence, Shining Armor, and the Doctor. She couldn’t focus on all three at once with her magic. She fired two magical bolts and intercepted them, and jumped in front of the Doctor, taking the third bolt. It hit her chest, and she immediately went down.

“Twilight!” Cadence exclaimed.

Twilight groaned in pain as she tried to stand on her hooves. Shining helped his sister to her hooves and hugged her for the first time since the mirror trip all those months ago. Rarity grinned as she towered over the injured princess. “Yield!”

Twilight rose to her hooves. “Rarity, please snap out of it. You can do it!”

Rarity laughed. “I fell for that once, but I have learned. No amount of Rarity’s magic or your friendship will save her! Yield, or your brother dies!”

Luna flinched at Rarity’s foolishness. Rule number 1 of anything is: do not threaten family. Twilight charged up her horn. “That’s one.”

Rarity was confused for a second, but she fired a magic blast at the princess of magic. “Two.”

Another magic blast hit the princess. “I said yield!”

Twilight looked up at Rarity, and smiled. “Three.”

Immediately, Twilight took the offensive. She fired magic spells left and right, sending Rarity back. The unicorn attempted to throw defensive spells, but Twilight’s magic was too strong for any low-level shied spell. She felt all the power from Twilight, and the darkness inside was actually scared out of her mind. Twilight continued her barrage of stunning spells, attacking the physical Rarity. While a part of her tried to hold back her attacks. It would take a lot of power to force the darkness out of her completely. Besides, with the walls between Rarity and the darkness thinning, the chances of Rarity being freed were skyrocketing.

Rarity stumbled as the last magical blast hit her. Her eyes were shifting from green to blue, but the green was winning back control. Twilight knew this would happen, and with Rarity struggling to the surface, the next step of her plan was being put into effect.

Rarity fell. The darkness within her was fighting to keep control, but Rarity was fighting back. Twilight smiled. “Ok, now it’s time to give me my friend back!”

At that moment, Rainbow Dash flew out of the box and stamped a necklace onto Rarity. At first, she shrieked at the sudden intrusion, but shrugged it off after realizing she put on a piece of jewelry. It was a gold necklace with an array of emeralds as the pendants. “Did you really think that a simple necklace will stop me?”

Twilight shook her head. “No, but that’s because it isn’t just a necklace.” She fired a magical blast at the necklace, and it transformed. The emeralds all morphed into one single gem, and with a slight color change, the gem turned red. Both Rarity’s recognized it immediately: it was the Fire Ruby.

Rarity was in shock. “Rarity, I know you can hear me right now, and you need to know this. We need your help. We all do, and we want you to just come back home. Please, Rarity, come home.”

Tears began to form. “Ho-home?”

Rarity’s horn exploded with magical energy. Twilight and the rest of the crew shielded themselves from the blast. “Twilight!”

The alicorn looked into the epicenter of the blast. There was Rarity with two heads. One had a face of concern while the other had anger.

“Twilight, help me!”

“NO!”

The two Rarity’s faced eachother. The dark magic Rarity swung her hood, nailing Rarity in the muzzle. Rarity tried to fight back, but Twilight knew she couldn’t. “Return to me!”

“Rarity, you have to fight it!”

“I can’t!”

“Rarity, think about all the ponies who need your help! Think of Spike! He’s under Nightmare’s control, and if we don’t stop them fast, who knows what will happen to him. Who knows what will happen to all of us. Please Rarity, you’re stronger than this,” Twilight said.

The dark Rarity raised her hoof and brought it down. Before it could land on her, a magical hold was placed on her hoof. “That. Is. ENOUGH!”
She threw her own hoof away and fired a beam of magic into the muzzle of her dark counterpart. The dark Rarity screamed as her form. cracked. “I am one of many! YOU CAN’T STOP ME!”

The dark Rarity’s form shattered into billions of pieces. The magical field dimmed as the winds died down. Rarity’s eyes rolled up into her head as she slumped down. Luckily, Rainbow Dash was there to catch her. Twilight sighed as at least one of her friends was saved.

She turned to the Doctor. “Will she be alright?” she asked.

The Doctor came over to her and performed a quick inspection. “Yes, she will just rest. Your attacks were focused on the dark force within, absorbing all of the hits. You never struck Rarity down at all, but I think we should avoid doing the same to your other friend, Applejack right?”

Twilight nodded. “Ok, Rainbow, help Twilight bring her in. Shining Armor, Cadence, I can drop you both off at the borders of the Empire. I’ve had a small army amassed there for you to take back the city. If you manage to drive Sombra out, wait until the right time to activate the Crystal Heart.”

Shining nodded. “Ok, two friends down, 3 more to go. Oh boy. Ditzy, I may need an extra cuppa tea before we hit the Vortex!”

“Gotcha!” Ditzy called from within the TARDIS.

“Now little pegasus, don’t be shy, add the sugar and reach for the sky,” Zecora said from within.

“Why am I doing this?”

“The cups of tea are above, and I do not have the wings of a dove. You will reach and I will watch, as the tea is prepared with scones in a
batch.”

The Doctor was going to have a headache with Zecora before they finish their quest.

Applejack

Applejack gave one last good buck before the tree came down.

With the taste of the apple treat she had to endure while masquerading as Princess Cadence, Queen Chrysalis ordered that many of Equestria’s apple orchards had to come down for good. Any pony who had great strength were ‘hired’ to bring them down. In return, she would not bring harm to them nor their families. If that didn’t work, then classic hypnotism worked best. Still, Chrysalis kept her word and brought misery to those who resisted.

Of course, Chrysalis had another motive. By threatening the lives of a pony’s loved ones, the love that Changelings fed on would be exposed and make it easier for Chrysalis to feed her hive while also ridding the world of the horrible red and green orbs that she had the displeasure of tasting. Feeding off Applejack’s love of her family and friends was almost too easy for Chrysalis, and it was a meal that was still being passed around.

Applejack was working in the orchards of Appleloosa bringing down the trees. Because of her experience and strength, she was best qualified for the demolition. She and a few other ponies worked together to bring them down, and high in the gorge surrounding the orchard, were the Changelings watching their workers bake in the eternal darkness that Nightmare created.

As the tree finally rested on the ground, Applejack breathed a big sigh of relief and felt pleasure. Her sickly green eyes glowed with the power the Changelings used on her. She surveyed her work in front of her. So many of the apples were smashed under the weight of the now dead tree. As she surveyed her work, she noticed a simple red apple on the ground, completely unharmed. No sign of bruising or anything.

Applejack walked over to the perfect apple, and smashed it with her hoof. She had her orders. No apple gets any mercy.

As the apple farmer turned to tackle her next tree, she found herself face first into a pair of wooden doors. She hit the doors with such strength, it wiggled. She bounced right off and landed on the ground. Her Stetson flew into the air and landed nearby…next to another perfectly fine apple.

Applejack groaned as she looked up at what hit her. It was a big, blue box. That was it. A simple blue box with window panels and a pair of doors. Above the doors and window panels was a black bar with the words: POLICE PUBLIC CALL BOX. At the very top was a simple light bulb.

“Well that can’t be right,” Applejack said to herself. “That wasn’t there a minute ago.”

Boy was she right. She walked around the box, looking for whoever put it there in the first place. She knocked on it in several places. It was 100% wood. It also looked pretty heavy. Applejack did another walk around just to ensure she didn’t miss anything. Aside from the handles, there was nothing else abnormal about it.

The pony reached for the handles to see if the box can open, and before she could push the doors, they flew open. Applejack jumped a few feet back as a brown pony walked out. He had a messy brown mane and wore a long, brown coat. Sticking out of the pocket of his coat was a silver stick with a blue tip. She thought the stallion looked weird wearing something so…outstanding. And not in the best way too.

The stallion closed the doors behind him. Applejack could swear she saw something inside. Before she could say anything, the stallion spoke.
“Hello Applejack,” the pony said.

Applejack raised an eyebrow. “Who are ya?”

“I’m the Doctor.”

“Doctor what?”

The stallion chuckled. “Just ‘The Doctor’. Nice to meet you,” he said.

Applejack sighed. “What do ya want? No, don’t answer. Leave!”

The Doctor sighed. The Changelings had a lot of control over the farm pony. The Doctor had managed to convince Twilight that he was going to snap Applejack out of her hypnotic state. The Time Lord took a step toward her, but Applejack took a step back. “Don’t come any closer! Ah’m warning ya!”

The Doctor stopped. “Applejack, calm down. Look, I don’t want any trouble, I just want to talk to you.”

“Yer interruptin’ mah work in case ya didn’t know,” she said. “Now git, or ah’m callin’ them Changelings.”

The Doctor chuckled and inched closer to the apple farmer. “You won’t do that. I know you won’t drive me away because deep down you need my help.”

“If yer a doctor, then ya should know there ain’t nuthin wrong with me at all. Ah’m perfectly fine!”

The Time Lord shook his head. “I don’t believe you Applejack.”

The apple farmer looked around frantically. She spotted an apple on the tree she knocked down and threw it at the Time Lord. The apple harmlessly bounced off his chest and rolled away. “An apple a day doesn’t always keep the doctor away, just so you know,” the Doctor said.

Applejack growled. “Just leave me alone, doc. Why don’t ah just spare y’all the trouble and git! Why don’t ya leave like the rest of ‘em!”

“This caught the Doctor’s attention. “Like who?”

“Like Twilight.”

Inside the TARDIS, Twilight was overhearing everything. When Applejack used her name, the princess of magic felt like she was frozen. Rarity, who had recovered from her earlier fiasco, was also overhearing the conversation.

Rarity had completely recovered from being Sombra’s puppet. The armor she was forced to wear was now gone and the effects of dark magic was completely wiped out. It was as though nothing happened to her, but she knew very well that Sombra used her the way no pony should ever be used. It made her feel dirty to take an empire for the wrong cause.

“Why did she say your name, Twilight?” Rarity asked.

“I don’t know. I didn’t leave her or anypony like I abandoned them,” she said. “I stayed as close as I could.”

Ditzy and Luna both looked at each other. “Perhaps this is not for us to be involved in, wouldn’t you agree?” Luna asked.

Ditzy nodded. Together, the two friends left the control room in search for something to pass their time. Zecora had been dropped back off to Ponyville after recovering Rarity for, what Twilight called, the right moment to strike. Zecora didn’t know what to think of that in the beginning, it made perfect sense that Twilight wanted her to help organize a rebellion against the Four.

The Doctor sighed. “Why would Twilight be involved in this? She would never leave you.”

“Yeah she would! She’s a princess now! A fancy pony with wings and a horn! She’s practically a god now, and why would she want to hang around us when she could be with the princesses performin’ their royal duties in elegance? We ain’t nuthin to her!”

The Doctor immediately walked forward, this time with no resistance from the hypnotized pony. “Well, don’t say that. Yeah she is an alicorn now, but that doesn’t mean that she—”

“She’s immortal, aint she?”

The Time Lord took a minute to think about the question. “Twilight will probably live her life with us, and when we die, she’ll forget about us! Ah though we were going to be friends forever, but that can’t happen if Twilight is living for thousands of years! First mah parents die, now my friendship with Twilight will die. Ah’ll never get to see Twilight like she’ll see me. Ah’m going to be old and a granny while Twilight will look the same as now. Ya don’t understand what it feels like to know your friends will forget about you and you can’t do anything about it.”

Twilight froze inside the TARDIS. Rarity was also frozen when she heard that Applejack was telling the Doctor what she was thinking in the past few months. She did fear that Twilight would outlive her, and she had talked to the others who all shared the same fear.

The Doctor sighed. “Well, don’t assume that,” he said.

Applejack looked up at the stallion. “You think she will forget you when she hits the millennia mark? That’s impossible, Applejack. I’m 904 years
old and I remember all the faces I’ve met over the years.”

The Doctor’s expression darkened. “All the faces I lost. All those ponies didn’t deserve to be put in harm’s way.”

Applejack sat up. “Yer not 904 years old. Ya ain’t an alicorn!”

The Doctor shrugged. “I’m not a pony, per say. I’m a Time Lord, and my race has the ability to live for long periods of time, unless they regenerate. Listen, I cannot say for sure whether or not Twilight is immortal, but that doesn’t mean you should abandon your friendship with her over the possibility that she might be.”

Twilight’s heart raced. “I’ve seen a lot of things in my 900 years of time travel. I’ve met spectacular people and ponies within that time. I grew attached to each friend I made, but I had to accept the ugly truth: it won’t last forever. You think it will last forever, the friendships, but they don’t. They wither and die just like everypony else, but that’s in the eyes of immortals. Immortals will see the birth and death of whoever they come across. They can’t fall in love because it is temporary. They can’t have a family when only one or two of your foals will regenerate.

I’ve lost so many of my friends, they all are blurred now. Their lives are racing away, tackling new obstacles and combatting old sins. They’re also living. They find love, they have foals, and their foals will later have little ones. It’s an adventure to see where life takes you, but if you are frozen in time, like myself, it’s nothing more than looking into the window of a shop and imagining yourself with the item, but you can never have it. It’s cruel.”

Twilight’s heart broke. “If Twilight is immortal, then you got the better end of the deal. She can live her life for a long time and can probably do a lot with her free time, but you, no. You can continue living on the farm with your family, settle down and find somepony to share your life with, have a family started, and overall enjoy life. You can do whatever your heart desires and it will be enjoyable because you will know that it will end soon. That’s the meaning of life. We don’t try to avoid death because we fear it, we avoid it because there is still much to do. What’s life without end?”

Applejack sniffled. “Don’t think Twilight will forget you. You made a lasting impression on her, you all did. How can somepony forget who her extended family is? You all will hold a special place in her heart. Don’t let time boss you around.”

Twilight moved herself from the door, allowing Rarity to continue listening. She was going to have a talk with Princess Celestia when this was all done. While Rarity stood by the door, her mind began to race. The Doctor was letting on more than what he already shared. 904 years old?

Applejack’s eyes began to water. The green glow that symbolized the hold the Changelings had disappeared, giving her free will. She ran to the Doctor, and gave him a big hug. The Doctor smiled as he returned the hug. The first thing Applejack heard was a series of drumbeats.
They seemed to be coming from inside his chest, where his heart was supposed to be. Even though it was troublesome to hear the foreign sound, it was relaxing. Listening to a heartbeat was soothing as it was, but this drumbeat was something else.

The two broke the hug. “I think you are all well. C’mon, we should continue looking for your friends.”

Applejack nodded. “Um, is Twilight alright? The girls?”

The Doctor nodded. “Um, can ya not tell ‘er about this?”

“Keeping secrets is my specialty,” the Doctor said. “Ok, so you, Rarity, Rainbow Dash, and Twilight are all secure. Now, I understand there are more.”

Applejack nodded. “Ah think ah know where they are. Do ya know how to get there?”

The Time Lord smiled as he knocked on the doors of the TARDIS. Rarity took that as a sign to get out of the way. The Doctor threw open the doors. “Care to step inside?”

The earth pony looked inside, and already her mind exploded. The console room was inhabited by Rainbow Dash and Rarity, who were both talking. When they saw Applejack, they both dropped whatever else they were doing and reunited. Applejack’s heart began to fly as she embraced her friends once again. As they united, the Doctor looked around for Twilight. He knew talking to her about the whole situation with immortality would be a sore issue.

"Twilight!"
The Doctor turned around. Twilight had appeared from wherever she was and embraced the apple farmer. There were just two more ponies left to reunite the Elements, three if rescuing Princess Celestia counted. Of course it counts, the Doctor thought. If anypony else can help us out, she can.

The Doctor returned to the console and released the brakes of the TARDIS.

“Ok Applejack, I’m going to need your best guess. We got ourselves ponies to round up.”

Celestia, Fluttershy and...Pinkamena?

Fluttershy was bored. So, so bored.

Shortly after she, Pinkie Pie, and Princess Celestia were thrown into the dungeon, Fluttershy developed a need to talk to somepony. Her blindness, a result from Nightmare Moon’s magic, left her with a desire to talk. Of course, Pinkie fell silent as soon as the keys were thrown away while Celestia was slipping in and out of consciousness due to her injury. With the guards all the way upstairs and no other forms of life downstairs, Fluttershy found herself talking to the wall.

After a while longer, she too became silent. Occasionally, Celestia would awaken and speak to the pegasus. It made them both happy. Fluttershy would talk about how her animal friends would sometimes chase Rainbow Dash around, especially the flying creatures she denied having as a pet. Some seemed to hold a grudge after the whole 'Find a Perfect Pet' contest Rainbow hosted a while ago. Celestia laughed and explained how she came across her Philomena.

"If you ever consider getting a phoenix, remember to keep its ash tray cleaned and ensure she is properly fed. Also, if he or she goes through their burning cycle, don't let them stay perched on your head when they burn up," Celestia warned.

Eventually, however, Fluttershy returned to the silence she had grown accustomed to. She began to bat at her own tail and occasionally hum some tunes her songbirds played, excusing the cursing in some of their songs. Some of the tunes were familiar to the princess, and soon they hummed a duet.

And then Fluttershy ran out of songs to hum.

As Fluttershy stayed silent inside her cell, Princess Celestia contemplated her situation. Her horn was broken and her Magic Core was exposed. Celestia was beyond worried now concerning the safety of the ponies in the room.

Celestia remembered Starswirl’s findings concerning the Magic Core. It is said that a unicorn has a horn, not just for show, but because of the unique and small power source within that had the ability to generate pure energy. The object weighed no more than a feather, yet it carried a lot of power. If a horned pony cracked their horn to the point where the Magic Core was exposed, the wrong move could jeopardize half a county. The devastation depended on the power of the horned pony.

Remembering the truth of the matter scared Celestia more than anything else in the world. Well, almost. A lot of things could go wrong if the necessary precautions were not made. The Magic Core was one of those.

Celestia should’ve gotten out easily, but thanks to Nightmare and Chrysalis, the guards believed they have detained criminals who attempted a coup. The emergency protocols that the guards had to remember by heart kept Celestia’s magic at bay thanks to a magical field canceling any spell made within.

The Solar Goddess began to wonder if Twilight was still alive. The Elements are the only thing that could save them from this awful nightmare. If Twilight didn’t survive, then hope is lost.

The more she thought about the Elements, however, the more she began to wonder where they came from. The first time she saw them was after the Doctor and Starswirl told them where to find them. Upon arriving to the Tree, however, Celestia felt like she had seen them before.
Thinking about them now, Celestia knew that she would have to search for the answer to the question: when did I first see the Elements?

Her concentration was interrupted by the sound of a wheezing machine. Celestia’s ears perked up. It couldn’t be—

Celestia rose from the floor of her cell, cautiously while doing so. Indeed, the magical blue box was starting to materialize in front of her. Next to her, Celestia thought she heard Fluttershy squeak in fear as the sound grew louder. Celestia smiled. She first heard the sound…well, it was a long time ago.

The blue box finally took a solid form. Celestia’s heart began to race. The doors of the wooden box opened, and bathed in a white light, the stallion emerged. He was brown, unlike the last time she saw him. His ship also looked different. New or old TARDIS, she could never fully tell. What she did know was her favorite Time Lord was back.

The stallion ran over to Celestia’s cell. “Princess Celestia!”

“Doctor! Oh mother of Me, it’s good to see you again,” she exclaimed. “New regeneration?”

The Doctor looked down at his body. “No, I’ve been this way for about 300 years now. Jumping from place to place though, never staying in one time. It gets boring.”

“At least you get to cheat. I have to progress the long way around,” Celestia said.

The Doctor chuckled and reached into his pocket. He pulled out his Screwdriver and began working. “Coast is clear, come on!”

Celestia looked up, more ponies were walking out. Applejack and Rainbow were both the first to exit. Rarity followed suit with the gray pegasus behind her. Celestia remembered her as the mare who almost caused the recent Summer Sun Celebration to go out of control.
Although it was never proven that it was Ditzy who released the bulls from their pens.

At last, Princess Luna exited with a familiar lavender alicorn behind her. Celestia’s eyes watered. Her student was one tough cookie to crumble. Besides from the unruly mane style she was sporting and the bandages on her wings, she was in good shape.

Cookies sound good right now, Celestia thought to herself.

The sound of a turning lock drove her out of her thought. The cell door came open and slowly opened. Celestia was able to slowly crawl out of the cell before losing her stability due to her injury. Luckily, the Doctor was nearby and caught her before she hit the ground. Her broken horn was still affecting her. It had felt like somepony got a bowling ball in a bag tied onto the tip of her horn. Not the little foals bowling balls, but
the ‘25’ pound ball. Already she began to bleed from the fracture.

The Doctor looked up at her horn. “Hmm, basic fracture, magical leaks are starting to arise along with, it appears to be added pressure. Magic Core is exposed so you cannot meet any enemies on the battlefield until you are properly healed,” he said.

Celestia nodded. “Ok, Luna, help your sister to the infirmary. Make sure she is given antidote number 15, put a kettle on and make sure she has her Jade tea made exactly the way she likes it. Also ensure that Earlhart the Brave’s fast healing potion is administered to the point where the splinter is deepest to avoid any overgrowth. I’m sorry Luna, but there won’t be much to do about her horn.”

Luna nodded and took her sister. Together, they walked into the TARDIS. Meanwhile, Twilight and Rarity were both trying to break the magical seal over Fluttershy’s cell. It appears as though Sombra had taken precautions in locking up members of the Elements. The seal itself was already weakening as the Doctor raised his Screwdriver up.

The field began to grow visible. Twilight and Rarity focused on the hinges while the Doctor focused on the lock itself. Eventually, the field began to falter as the three continued to concentrate at the task at hand. Er, hoof. Finally, the field fell, leaving the cell wide open. Fluttershy, still blinded, began feeling her way out of the cell. Finally, she bumped into Rarity and Twilight. The girls all hugged each other, and soon
Applejack and RD followed.

The Doctor and Ditzy smiled. 5 down, one to go, the Doctor thought.

After a while, the 5 began to settle down. “Ok, all we need now is to find Pinkie.”

“She should be here. I heard her a while ago,” Fluttershy said.

The girls all looked around the prison. The Doctor began to inspect one of the cells when he heard scratching on the cell walls. He followed the sound to a cell shrouded by darkness. Without magic, the Doctor knew there was a powerful force surrounding the cell.

The sound of Pinkie’s giggling filled the prison, but it didn’t make anyone else feel happy. In fact, there was fear in the room. The Doctor was sure this was the right cell. He placed a hoof onto the cell door, and a face slammed itself onto the bars. It was Pinkie Pie.

Aside from her usually fluffy, but now flat mane, the wicked smile, and the bulging eyes that stared into your soul, nothing was different from the earth pony baker. From the force of her slamming into the bars, it almost appeared she was halfway from squeezing through the bars.

Twilight became alarmed and she came over to Pinkie’s cell. “Pinkie? Are you OK?”

Pinkie turned her attention from the Doctor to the princess for a moment. “Why wouldn’t I be? I mean, after all, I was the last to be rescued.”

Pinkie smiled. “So, this is Princess Twilight Sparkle? The bearer of the most powerful Element in Creation? The prophecy mare? The future ruler of all Equestria and outer colonies? The prodigal student to Princess Celestia? Eh, I expected a strong and fearless hero, not a unicorn with giant Post-Its that look like wings.”

The alarm began to blare in Twilight’s mind. The ‘Prophecy Mare’? What does that mean? She sounds like we’re just meeting for the first time.
The Doctor looked uneasy in the corner of Twilight’s vision. “We didn’t know where you were,” Twilight said. “We’re here to help you Pinkie.”

Pinkie giggled. “Oh, and stop calling me Pinkie. That was a name given to me by simple foals who wanted a cheery name to go with my face.”

“Then what can I call you?” The Doctor asked.

Pinkie kept her glare at Twilight. “Pinkamena is fine. You know, for as long as I have been in Ponyville, nopony has ever asked me my full name, and I am quite sad about that. I am Pinkamena Diane Pie, overseer of Sugarcube Corner, former rock farm, full-time master party planner and bearer of the Element of Laughter. Ha! Boring, isn’t it? As for you, Doctor—”

She turned again to the Time Lord. “Names are important. They define you and you should know that. Names are powerful, Time Lord! Why is your name shrouded in time? Why is your name the most dangerous word in the Universe? Why do you call yourself ‘Doctor’? Doctor who?”

The Doctor came closer. “The Doctor has a name, and it is a secret he will take to the grave. Coming soon to a Universe near us, the question will be answered.”

The hairs on the Doctor’s neck rose up. Pinkamena started hopping around in her cell, cheering loud enough for anypony worth their bits to notice. “The Doctor’s here! The Doctor’s here! And death will follow! The Dark Lord has come!”

The Doctor confesses

Author's Note

After looking back at the old version of this, I realized that I didn't do a good job with it and rewrote the entire second half. I'd say there are about 9 or 10 chapters remaining. Hang tight guys. Flutter On my fellow bronies!

The Doctor confesses

Ditzy looked at the pink baker in the cell with concern and confusion. Pinkie was dancing in her cell, repeating her last words. “The Dark Lord has come! The Dark Lord has come!”

Twilight looked over at the Doctor. He was nervous. The brave stallion who could run head on into an army was gone. All that was left was a coward. She was going to interrogate him later, at least without Pinkie in the same room.

Sorry, Pinkamena. The earth pony stopped her dancing and finally stood still. “Oh, and it looks like he has it all here. The TARDIS, the Sonic Screwdriver, the companion who doesn’t know that the stallion she has been traveling with is really a mass murderer who shouldn’t be alive, and the regret on his face. What’s wrong Doctor, am I upsetting you?”

The Doctor snapped out of his trance. “As a matter of fact, no. I’m just surprised you heard of me. I try to stay out of the history books.”

“I didn’t recognize you from the history books, dear Doctor. You see, one can learn a lot about a pony based off of their facial features alone. Wrinkles along the eyes suggest a pony always has a grin on their face. Probably has a good job and wakes up every morning happy to be with their special somepony. For you, dear Doctor, your name and crimes are written all over your face. Your life in those 900-year old eyes show great loss.”

Twilight looked at the Time Lord with interest. “Lord Doctor of Gallifrey is all alone now. So without a companion he once knew as a friend. So long ago, your friend turned against you. How sad of a day that was for you. Childhood friends turned enemies.”

The Doctor’s ears perked up. “Excuse me?”

Pinkamena waved off her remark. “Oh well, what has been lost will be found. Anyway, I am curious about a few things. One of them is how the war actually ended. I’m seeing various stories on how it ended, but one can never know for sure unless one asks the sole survivor. Well Doctor? I am wondering about the fate of that lost world. Dear Doctor, where is Gallifrey?”

The ponies in the room, minus Fluttershy, looked at the Doctor. “Any day now, Doctor. Somepony upstairs probably heard the TARDIS materialize and probably sending for a head of command. You don’t have the time to stall anymore.”

Silence from the Time Lord. “SPEAK NOW DOCTOR! CONFESS YOUR CRIMES TO US!”

The Doctor growled. “OK! I DESTROYED GALLIFREY!”

All the ponies in the room gasped. Pinkamena smiled as the Doctor came undone. “Please elaborate.”

The Doctor sighed. There was no way he was going to slip away from this one. “It was after the fall of Arcadia. I was in the front lines trying to drive back the Daleks. I found and destroyed a legion of Daleks, and that was when I had enough. The war was going to burn the Universe if I didn’t stop it. The Daleks were coming in by the billions every day. There was no way to stop them by fighting. The Time Lords had an arsenal of weapons locked away, and out of all of them, only one could stop the war. I had no choice.”

Twilight walked forward. “So instead of figuring a way out of the war, you destroyed two civilizations and survived?!”

“I had no choice! There wasn’t a way out. Either I let the Universe burn or destroy my own people. It had to end with my people, because they were about to destroy Creation if I didn’t stop them! I fought two demons!”

“And probably innocent fillies while you were at it!”

“I COULDN’T SAVE THEM!”

Twilight took a defensive stance. “I had no choice. I couldn’t save everypony. I had only one way out, and that was burn them. I burned my whole planet and its attackers! I wasn’t supposed to survive, but I did! I didn’t want to! If you had to make a difficult choice, and both seemed extreme, which would you take?!”

The ponies stayed silent. "Exactly. I didn't want it to happen, but I just couldn't let either of them get away. The Daleks would've destroyed everything without mercy. The Time Lords wanted to cause a great paradox to rip the Time Vortex apart. Imagine a blood vessel in your body, Twilight. A blood vessel near your heart. What if one day it just suddenly exploded. There was no warning and no way to recover from it. You would die, Twilight! If I let them get away with it, they would've destroyed Creation."

Twilight’s eyes flared up. “How many ponies died?”

The Doctor shook his head. “How many, Doctor?! If we are to trust you, tell us!”

“I don’t know!”

“YES YOU DO!”

The Time Lord lowered his head. “I can’t place an exact number. There were too many,” he whispered. “I didn’t want to live! I wanted it all to end, Ms. Sparkle! I had no desire to survive, but I did anyway! Not only did I lose my family, but I lost what it means to be the Doctor! I was no longer the Doctor the minute I joined in the war, and I certainly was no longer the Doctor the minute I destroyed my own people.”

The Doctor turned to the pink pony. “How did you know?! TELL ME!” The Doctor slammed his hooves into the bars of the cell.

Pinkamena giggled. “I see your past, Doctor. So many faces, so many lives. 904 years of running, and now it is time to stop. Your time is up, dear Doctor.”

“No, I won’t. These ponies need my help, and if I die trying, then so be it! I will not give up!”

Pinkamena smiled. “Don’t worry, you won’t sleep yet. You have one more destination to make, but it will be years before you get there.”

“Where?”

Pinkamena leaned in closer. “You will know when you get the call. The whole Universe will know.”

Pinkamena started to laugh. Fluttershy cowered as her friend lost more of her mind. “The Doctor will die once more, when he reaches Trenzalore!”

Pinkamena’s eyes rolled into her head as she collapsed onto the ground. All the ponies in the room gasped. Twilight moved the Time Lord out of the way and used her magic to open the door. It was safe to say that Pinkie was alright.

Granted she still isn’t insane. She turned to the Time Lord, who was quietly entering his TARDIS without a word. Ditzy stayed in the dungeon instead of following the Time Lord. She helped Twilight lift Pinkie from her cell and inside the TARDIS. The other ponies followed close behind. When the last pony was inside, the doors closed and locked.

The Doctor sat quietly inside his study.

The Doctor didn’t just hang around inside the console room like everypony believed he would. Whenever he wanted some quiet time, he would allow the TARDIS to drift endlessly in space, lock himself in his study, and read. He didn’t care what he read during his time, all that matter was he had something to keep his mind grounded.

In his hooves was a Daring Do book that he picked up during his time as Time Turner in Ponyville. Twilight never guessed that she checked out a book to a Time Lord.

As time went on, he went from reading an innocent Daring Do book to reading the History of the Time War, a book he kept in the library. He didn’t like reading through it, but at least he could recall and later surrender to the fact he committed genocide. He was adding salt to the wound willingly.

A knock came at the door. The Doctor looked up from his book. Who knows where my study is?

He rose to his hooves and opened the door. In the hallway was Applejack with her hat on the side. The Time Lord sighed but put on a fake smile to greet the earth pony. “Hello Applejack, what brings you here?”

The pony shrugged. “Ah just came out of the orchard, which was huge, and ah just thought ah could get some quiet time since RD was jumping in the swimming pool next door. Ah saw ya leaving, and ah thought that maybe ah can join you, if that ain’t too much trouble.”

The Doctor raised an eyebrow. “That was rehearsed.”

Applejack sighed. “Ok, ah wanted to check up on you. Ya took us out of that dungeon and just left without another word. Ah want to see how you are doing, and apologize for Pinkie’s behavior.”

The Doctor shook his head. “It wasn’t your fault, and it definitely isn’t Pinkie’s fault. That level of intelligence of the Time War doesn’t exist in this Universe. She probably overheard something Princess Celestia said. It is natural and I probably should’ve expected that. Besides, I’m fine,” he said.

Applejack narrowed her eyes. “Yer lying.”

The Doctor laughed. “That’s me, the silver-tongued Time Lord. If you want to come in, you can. I’m not stopping you.”

The earth pony nodded and entered the study. Her jaw hung when she saw all the stuff inside. There were dusty old books, walking canes, a large brown hat with a multicolored scarf, and a weird long piece of metal on a desk. At the end of the metal rod was a round, black piece. Aside from the rod, it felt like she was visiting old family members.

Applejack inspected the metal rod on the desk. Inside the round piece of the rod was glass. “That’s a Dalek eye.”

She immediately jumped back. “Don’t worry, it was an add-on. It’s officially a Dalek’s eye stalk. Inside a Dalek is a creature. The creature needs to see the outside world, so they use an eye stalk to see. It’s also a Dalek’s weakest point.”

“Why do ya have it?”

The Doctor sighed. “A souvenir from a very long day back in my Universe. The planet I used to protect was stolen by the Daleks, so I and my companions flew off to retrieve it, but the Daleks were destroyed before we escaped. This was all I had from that day,” he said.

Applejack looked back at the eye stalk. “Umm, Doctor?”

The Time Lord looked over. “How bad could it have been?”

The Doctor sighed. "It could've been bad for you. The Universe I was in has its own timeline. Well, it's not so much of a timeline but more of a ball of spaghetti noodles. Twists and turns all over the place. You can meet somepony for the first time but they already met you in the future. You can visit the dead, have tea with the ponies who aren't born yet, fight in wars long forgotten or rediscover age-old empires. That was and still is the beauty of time travel."

The Doctor walked over to his scarf. "This was a gift from an old friend. I traveled through time and space for hundreds of years and I've never gotten sick of it. Everyday is a brand new adventure and nothing can ever compare. If either the Daleks or the Time Lords had accomplished what they set out to do, all of that would be gone forever. Time would never exist and the ripple would've affected so many other universes."

Applejack walked around the study, surveying all the little trinkets. There were Egyptian artifacts, alien ray guns that no longer worked, high heel shoes (the Doctor never could figure out why they were there), keys, a badge that said UNIT, a leather wrist band with a plaque that read 'Captain Jack Harkness. Do not touch! No, seriously Jack' and so many other cool things.

There was one thing that caught Applejack's attention: a photo on his desk. Upon closer inspection, she realized that it was the Doctor as a foal running with another. The pony was gray with black hair and he had an hourglass cutie mark with a snare drum next to it. The two foals in the photo appeared to be having a great time running through a red field.

Her curiosity caught the Doctor's attention. "I don't know if Twilight will ever trust me after hearing what I had to say, but it's the truth. Everyday since the end of the war, I've tried to right what was wrong. Gallifrey is gone, and I'm all alone in the Universe. I will give 110% of my power to help you regain your world and that is my promise."

"That's very nice to hear, Doctor."

The two ponies turned to see Twilight standing under the doorway. She was trying to look angry but there was no way she could keep a frown. "I thought about what you said, and what you told Applejack just now. While genocide is frowned upon, especially in my book, I can see why you had to do it. You hurt yourself more than you hurt those Time Lords who burned. I don't think I can ever wrap my head around the idea, but I will have to."

The alicorn princess approached the Time Lord. "We need your help, Doctor. Help us Doctor. What Sombra and the others have done is too great for me to comprehend. If anything we need you to lead us to victory. I trust you."

The Time Lord smiled. He walked over to his desk and opened a drawer. Inside was a large map of the kingdom of Equestria. "If you have the connections in all the major cities, make contact immediately. If we can divide Sombra and Nightmare Moon's forces, we can get a clear shot into Canterlot without a problem."

Twilight nodded. "For a thousand years, the peace has been kept in this world. Now they have squandered that peace and moved right on in with Nightmare's eternal night, Sombra's empire and Chrysalis' desire for love magic. It's time to go to war."

Taking Canterlot: part 1

‘Call in an army’? Sure, Twilight will send out a scroll to her brother and all her contacts across Equestria and organize a well-planned coup against the four overlords of the country. With one a Changeling queen who is bent on feeding her hives with all the love in Equestria, an alicorn who only wishes to have the ponies of the realm respect her eternal night, a unicorn who rose from the dead and learned the remaining 1,000,000 words in the English language and a snake-like trickster who absolutely hates organization, a coup would be easy for the Princess of Friendship to plan.

For some strange reason, it actually was easy.

Thanks to the Doctor, many of Shining’s royal guards were found and unhypnotised. With more than enough to take back the Empire, the prince waited for his wife to finish the conversation she was having with the Time Lord. Thanks to a spell in his library, the Doctor had given the royal family the right spell to send messages via magical links. This made it easier minus the baby dragon who used to send letters to Celestia from the 6.

Outside the borders of the Crystal Empire, Cadence sighed as she reviewed the Doctor’s plan. “Are you sure about this? We have found the Heart, and it may not be possible to restore it,” Cadence said.

“King Sombra only has a hold as long as he is in the Empire. Right now, he isn’t. If you can get to the Crystal Heart and cast the right spell on it, you should prevent it from being cursed in the event he tries to return. Just keep it within your magical hold until I give the word. When that happens, activate it,” the Doctor said.

Cadence sighed. “Very well. How are my sister-in-law’s friends? Have they all been recovered?”

“Yes, and they are eager to get some payback for Sombra’s little stunt. Believe me, Canterlot is falling tonight.”

The Princess of Love smiled. “Fantastic. We will be waiting for your cue.”

“Good.”

Meanwhile in Canterlot Castle, Sombra untwisted his tail and cursed as Discord laughed his snake-like butt off. He had dragged the king of shadows halfway across Equestria without realizing it, then took the longest route possible just to bring him back to Canterlot. Chrysalis also tried suppressing her laughter while Sombra cursed the god of Chaos.

“Through the Unicorn Range, Discord? You had to drag me through that damn range?!” Sombra boomed.

“I’m trying to have some fun here, in case you are unaware. See, I got Chrysalis to laugh at you behind your back and Nightmare has only made eye contact at me. I succeeded in making this boring takeover interesting!” Discord said as he continued to laugh. “You should’ve seen your face when we flew into the desert!”

“A cactus! You flew me straight into a bucking cactus!” Sombra raged.

“Go pull pricks out of your ass,” Discord remarked.

Sombra snorted. The Changeling queen shook her head. “I was not laughing behind your back, in case you want me to make that clear,” she said.

“Thank you.”

“I was quietly chuckling at the cactus needles sticking out of your flank,” she said.

Discord lost it. He continued to laugh as Sombra charged his horn. With a blast of dark magic, Sombra’s one tooth turned into goo. Discord stopped when he realized he was choking on his tooth. With a snap of his claw, his running tooth hardened and returned to normal.

Sombra smiled as Discord gave him a disgusted look. Then, he smiled as he realized that Sombra pulled a joke on the god of Chaos. Chrysalis smiled as she sipped her beverage. Her servant, the baby dragon Spike, had given her a tea found in Celestia’s private kitchen. A kitchen, she later found out, filled with various cake recipes, including something called the MMMM. She had no idea what it was, but if Celestia were to return, she would go to this recipe. She hid it in the vegetable drawer in Luna’s kitchen.

“Dear dragon, bring me more tea!”

“Yes mistress,” Spike said.

Discord looked at the two interacting. While he made his choice to take Equestria over, he felt almost guilty of doing so in the first place. That small part of his mind screamed at him, telling him to go back and fix everything, but he knew that was impossible. All the villains in the room would rip him apart should he suddenly turn his back on them.

A bright light illuminated the room which they were all in. Nightmare Moon appeared, and she was not in a pleasant mood. “Discord, you have some explaining to do,” she said.

“Hot chocolate volcanoes were not my idea entirely. I found it enjoyable after a pony said that chocolate milk rain was not considered chaotic,” Discord said.

“Not that! Wait, what?”

Chrysalis looked over at the god of Chaos. “Hot chocolate volcanoes?”

Discord shrugged. “It’s a popular beverage in the winter, but its spring right now.”

Chrysalis face-hoofed. “Anyway, I’m talking about the walls of Canterlot. There are a bunch of ponies out there calling for you.”

Sombra raised an eyebrow. “Ponies know about you?”

Discord chuckled. “Yeah, um, I may’ve had some contact with the residents of Ponyville in the past. They may know more about me than I let on," he said.

Blood started to rush to Nightmare’s head. “YOU SOFT-HEARTED FOOL! YOU ALLOWED YOURSELF TO GROW WITH THEM?!”

“Like I had a choice! It was either be released from stone and conform to them, or remain in my prison and you all would’ve never been here, drinking the golden drink that is victory!”

“I’m going to pretend you didn’t compare our victory to a golden drink,” Nightmare said. “Just get out there and deal with this!”

Discord rolled his eyes and teleported to the outer walls of the city. When he appeared before his pony citizens, he was almost nailed with an empty tin can. The can, somehow, was thrown with a stone in it. The draconiquus smirked at the weapon and looked over. It appeared as though all of Ponyville came to the city.

The god of Chaos scanned the city. He smiled as he noticed the Mayor of Ponyville leading the crowd. “Discord! Can you hear us?!”

“NO!” he responded.

Nopony cracked a smile. “Discord, we demand that you open the walls of the city! We want our princesses back!”

Discord laughed at the Mayor’s demand. “And what will you do if I don’t!”

“Then we will come in ourselves!”

Discord froze. That wasn’t the Mayor. On the ground, ponies parted like the Red Sea, and two ponies took the front. One of them was Trixie without her magician’s hat. The other was a pony with a snow-white coat and an electric blue mane. The pony wore a pair of magenta glasses and had a wild grin on her face.

The draconiquus smirked. “Trixie Lulamoon. I see you formally declined my invitation to the party. I see you also made your choice when it came to unlimited power!”

Trixie sighed. “Trixie made her choice a long time ago, Discord! Trixie chose her fellow ponyfolk over you fake gods! Trixie will not force her brothers and sisters to bow to her again, not after the Alicorn Amulet scandal that tarnished her image.”

“You tarnished it a long time ago, Mediocre and Weak Trixie. Besides, what power do you have to burst through this wall?”

Trixie’s strength in her stance nearly diminished. Twilight had asked for her help, even though she had little legitimate power, but damn it all to Celestia she was going to do whatever she could. She reformed her stance and smiled. “This time, Trixie does not have the power to bust through. Trixie would like to introduce a pony who had a similar beginning as Trixie. A very old friend of mine, whether you believe it or not. Behold the DJ Pon3, Vinyl Scratch!”

Vinyl cheered as her name echoed up the wall. “Thank you for having me, Trixie!”

“Trixie is honored to have you here!”

Vinyl laughed. Discord laughed harder, and that grabbed the pony’s attention. “You brought a DJ to break these walls? Oh that’s rich! What is she going to do, spin some tracks?!” he laughed at his own joke. “This is DJ-Pon3 and I am here to say: tear down this wall! My lyrics don’t rhyme ‘cause don’t you see, I have no real musical talent!”

The DJ’s smile faltered. She was just insulted. “My friend Trixie, I need your help. I need the black suitcase that’s back there.”

Trixie smiled. “The Great and Powerful Trixie will fetch your black suitcase.”

Discord laughed even harder. “If you get it quick, maybe she’ll toss you a bone!”

Trixie disappeared into the crowd, and later returned with the case that Vinyl wanted. The DJ thanked the magician as she set the case down. The draconiquus looked down at the case. It was a long and rectangular suitcase, and it looked like it weighed a ton. The DJ smiled up at the god of Chaos. She unclicked the locks on the suitcase and waited for Discord to stop laughing.

He looked down at the DJ. “And what, pray tell, is that?”

Vinyl smiled. “Oh, it’s nothing special—”

The lid flew open as Vinyl hoisted herself on two hooves. Using her magic, Vinyl lifted the object inside. It appeared to be a minigun in structure. It had two record players attached to both sides along with dual speakers. The barrel of the weapon was long and painted white like the owner. The two chambers at the end were stereos. Using her magic, she locked two mechanisms to her hooves and raised the barrel of the gun at the wall.

“It’s just my Bass Cannon!”

With a flick of a switch, the weapon charged up. The two records on the sides started turning as a song began playing. When the bass dropped, however, the walls of Canterlot were blown apart by a wave of pure energy. The bass escalated as the energy blast impacted the wall. Discord and a few other guards were sent packing as the concrete wall caved in. Vinyl’s newest track began playing as more of the wall fell.

Discord screamed as he flew through the air. The Draconiquus turned to the reader with a confused expression. "I thought she was a mute!"

Trixie reared up with her horn charged up. “CHARGE!”

All the ponies in Ponyville roared in response, and they all stormed the city. Slowly following the crowd was the DJ continuing to fire her Bass Cannon at the structures within that were built by the Shadow Ponies. Discord teleported to safety, but he knew that nowhere in the city would be safe. He looked up into the sky, and it was filled with Pegasi flying in from Cloudsdale. The draconiquus did a double take when he noticed some of the Pegasi carried unicorns with them.

Without a second to think, Discord teleported back into the throne room with the other 3. Sombra screamed as Canterlot was quickly filled. Legions of Shadow Ponies and Changelings met with the rebellion, but were quickly overtaken by them. Nightmare Moon growled as she grabbed one of the Shadow Ponies nearby. “RAISE THE SHIELD OVER THE THRONE ROOM! DENY ANY ATTEMPT AT TELEPORTATION!”

“Y-yes your majesty!”

Chrysalis immediately grabbed Discord. “You promised me victory!”

Discord raised his claw and paw up in innocence. “This was not something I foresaw!”

“You swore there would be no resistance! How am I supposed to get what I want when there is a rebellion?!”

Suddenly, a magical window opened in front of Sombra. “Your Majesty, the Crystal Empire is under attack! It’s Shining Armor and Princess Cadence! We need reinforcements!”

Another window opened in front of Chrysalis. “Mother Chrysalis, Appleloosa has fallen. We request assistance!”

Another opened. “Mistress Nightmare, Manehattan has fallen! We’re getting slaughtered out here! We need reinforcements!”

Discord gulped hard. Chrysalis walked toward the window of the throne room. She watched as her Changelings were overrun by the ponies. She scanned the horizon, and her heart dropped. She could swear, that in the distance, a familiar blue box was flying through the sky. Behind the blue box was a swarm of Pegasi and unicorns. The city below was already overrun.

Chrysalis shook her head. “It’s him! It’s the Destroyer! The Dark Lord is here!”

Sombra looked over. “What are you talking about?!”

“My kingdom! In the old days, my hive was once an empire. We rose to take all of Equestria and feast on their love long before those Sirens did. He stopped us! He destroyed my clans and forced us to hide in shame!”

Discord produced some binoculars and trained them on the box. “The Dark Lord has returned! The Destroyer of the Changeling Regime! The Doctor is here!”

And headed straight toward them.

Taking Canterlot: part 2

Author's Note

This story is almost done, so I'll hopefully be back on Time Traveling Foal Sitters soon

Taking Canterlot: part 2

All across Equestria, ponies and other species who lived in Equestria were hard at work with the simultaneous rebellion that Princess Twilight organized. While she was the Princess of Friendship, war seemed to be easy to the lavender princess. With the right favors called in by her friends new and old, Twilight managed to pull together enough power to shake the foundation that was Sombra’s reign.

In the Frozen North, Princess Cadence and Shining Armor were hard at work leading their armies to attack Sombra’s regime. Crystal Ponies, instead of hiding away, armed themselves with whatever they could find and fought against the Shadow Ponies and Changelings keeping the darkness over the Crystal Empire.

With the walls of Canterlot busted wide open, Twilight opened the doors of the TARDIS. The sheer mass of ponies storming Canterlot brought her to near tears. Not of sadness, but of happiness. Even though they possessed the powers of the Elements, there is no force in the Universe that rivals the will of those who are willing to fight for what they believe in.

Ponies will do anything to protect their homes, even go to war, Twilight thought to herself.

With Vinyl breaking down the walls of the city, the princess learned to never doubt the musical, or engineering, talent of the DJ. She actually had to remember her for future events. Perhaps her musical talents could be put to good use.

The Doctor held tight on the controls. His brown long coat was flying in the wind along with his goggles. He had sent Princess Luna and Ditzy ahead to find the Elements of Harmony before they arrive to the throne room. His hearts were still beating rapidly as the plan they all devised still raced in his mind.

I am asking you all to trust me. Above anything, do not deviate from the plan, no matter what happens to me. This is your world, I am only helping you succeed, he told them earlier. The Doctor’s plan alone was enough to make the girls think he was crazy. He had planned to storm Canterlot with all their might and allowed the Doctor a window to stop the Frightful Four before it was too late.

What the Time Lord didn’t mention was that he had to do the impossible to ensure that everything went according to plan.

Twilight turned back to the Time Lord. “Are you sure about this?!”

“Yes! If your theory is correct, then there shouldn’t a problem! Once the Elements are reunited with your crown, they should reverse the damage it had sustained when you were defeated earlier!”

“Not about my theory, about you. Are you sure you can pull it off?”

The Doctor looked over. “Nothing is impossible, my friend. Just difficult to pull off.” The console started sounding an alarm. “Oh dear, it appears that Chrysalis and Sombra ordered a shield to drape over the North Tower leading to the throne room!”

“Can you get by it?”

The Doctor shook his head. “The TARDIS recognizes the wavelength over the tower. I swear, it is like the Black Archives back in London.”

“The what?” Twilight asked with her eyes glistening. Archives equaled information, and if Princess Twilight was anything like her older self, any chance at obtaining information was a chance worth pursuing.

“Nothing, just something I remembered from my old life. Well, one of them anyway. Ok, we are nearing Canterlot Castle. Applejack, do you have the rope?”

The farm pony looked up from next to the door. “Ah got it!”

“Excellent. That rope is made of an industrial material that is very durable. The material is from the Zygons whom I had battered from to get it. Turns out, they like gemstones. Anyway, lasso the rope onto the spire of the throne room and take out the guards. The combined force of the Shadow Ponies and Changelings have created a shield over the throne room. I can’t land the TARDIS until that shield is down. You will need to hold on tight!” the Doctor said.

“And I have that, right?” Twilight asked.

“That’s the idea. Ground yourself nearby the console and with Applejack in tow. Once the shield is down, we move in. Now, Rarity and Pinkie, I’ve supercharged your cannons so they shoot more ribbons and confetti. The ribbons have micro-transmitters and magnets on them, so they can seek and lock each other in case you need to wrap up a nice present. The cannons will not directly harm the Shadow Ponies, unfortunately, but leave that to me.”

Rarity looked at the Doctor. “But I don’t have a cannon,” she said.

The Doctor smiled. “Today you do. I want the both of you to work together in taking out the guards. Rainbow and Fluttershy should be leading the aerial assault on the castle,” he said.

“Strange that Fluttershy elected to lead the front lines,” Rarity muttered.

“Rule number one: never piss off The Shy,” Pinkie said.

The Doctor looked over. “There are rules?”

“Let’s not talk about that right now, Ok Doctor?” Twilight said.

The Doctor nodded. He then turned to Pinkie Pie, who was busy testing her brand new cannon. When the Doctor first suggested the idea of using cannons, Pinkie somehow got ahold of her personal Party Cannon and fired a celebratory shot. How she got it on the TARDIS was beyond the Doctor. “Are you feeling Ok?”

“Yeah, why wouldn’t I be?” she asked. “Well, maybe it was because I got tricked, imprisoned, mind-controlled and overall had a bad experience with magic beyond my control, but oh well! You win some, you lose some!”

“I wouldn’t call that losing,” Twilight muttered.

Rarity had ignored the conversation while inspecting her cannon. The Doctor said nothing and returned to the console. Waiting for him there was Applejack with her hat down. “And you? How are you doing?

Applejack shrugged. “Ah never had a problem.”

The Doctor gave her a look. AJ sighed as she put her hat down. “Ah’m still trying to come to terms with it. Are ya sure she won’t forget?”

“All of you made a lasting impact on Twilight. If she is immortal, or she follows the normal lifespan of alicorns, she will never forget you.”

“Ya haven’t met her in the future?”

The Doctor shook his head. “I’m speaking from an ‘immortal’s’ point of view.”

Applejack smiled as she hugged the Doctor once again. Twilight looked over at Applejack. While she understood what Applejack’s argument was, it was tough to digest the truth once spoken. Had her transformation, nay her apotheosis really changed Applejack’s opinion about her?

Pinkie looked over at Applejack, then at Twilight, then back at Applejack. Before she could say anything, Rarity’s hoof went to her mouth, keeping whatever Pinkie was about say in her head.

For now.

The Doctor looked all around. With Rainbow and Fluttershy leading the Pegasi through the air, the plan looked almost like it would work. If Ditzy and Luna get the Elements, then victory. “Well then, Allons-y!”

With everything in place, the Doctor floored the TARDIS. Applejack readied her lasso while Rarity and Pinkie readied their cannons.
Applejack had hurled her lasso at the spire of the tower. With Twilight’s magic, she was able to hold her friend down. With her strength and the Doctor’s flying capabilities, they launched themselves around the building. The Changelings immediately responded by firing at the TARDIS. Pinkie and Rarity approached the open doors and began firing.

Well, Pinkie did.

Rarity looked at the cannon she possessed. Except for the fact it was a weapon, it was neatly decorated with purple laces and ribbons. A series of gemstones were embezzled onto the barrel of the cannon in the shape of her cutie mark. On the top of the cannon was the trigger that appeared to reach whenever she pushed the button.

The fashionista looked at the Doctor, who was busy trying to keep the TARDIS from exploding. “But, I don’t even like cannons! They’re not in style, and they probably won’t ever be in—”

A blast of green magic flew into the TARDIS and struck a curl on Rarity’s mane. The unicorn watched as part of her well-styled mane became undone. Her eyes went wide as she turned her attention to the outside world. A few Changelings had clogged Pinkie’s cannon with a green goop.

Rarity looked at her messy mane. “You ruined my curls!”

Applejack kept herself from laughing. “Ohh. It.”

Rarity positioned herself behind her cannon. “Is.”

She grabbed a helmet from the nearby coat rack and placed it on top of her head. “ON!”

The fashionista approached her cannon and slammed on the trigger. A barrage of confetti blasted out of the cannon and completely obliterated the Changeling’s smile. They flew back as Rarity continued her attack while Pinkie removed the goop from her cannon. But Rarity didn’t need any help from the energetic baker.

The Changelings needed help.

As Rarity continued to fire away at the Changelings, an alarm on the console began to ring. “Shadow Ponies!”

“Can you fight them off?” Twilight asked.

The Doctor smiled. “There are a lot of things I do whenever I’m bored. One of those things is add a new modification to the outer lightbulb on the roof of the TARDIS. Just wait.”

As the Doctor talked, three Shadow Ponies began flying toward the magical blue box. Their mouths widening with their fangs bared for all to see. The Doctor saw them on his monitor, but he did nothing. All he had was a hoof hovering over a blue button.

One of the Shadow Ponies screeched loudly, alerting the alicorn princess inside. “Doctor?”

The Doctor held his hoof high. The Shadow Ponies screeched again, this time striking fear into all the ponies in the TARDIS. “DOCTOR!”

The Time Lord raised his hoof. “FLASH BANG!”

His hoof slammed on the button. The light on top of the TARDIS immediately flashed a bright light. The Shadow Ponies shrieked as the light blinded them, and destroy their physical form. Their former magical bodies were wisps in the air now. The Doctor laughed as the screeching of the Shadow Ponies faded into nothing.

Twilight was impressed with the Doctor’s work. With the last Changeling guard wrapped up like a Christmas gift the shield fell around the tower. Applejack released the lasso, leaving the Zygon rope dangling from the roof. The Doctor walked toward a panel nearby and pressed a button next to the speaker. “Rainbow Dash, Fluttershy, it’s the Doctor. Return to the TARDIS, we’re ready to move in.”

Who was that?! Came Fluttershy’s voice.

Ugh, we’ll be right there. C’mon Fluttershy, he even said his name!

The Doctor chuckled as he released the button. He looked over at Applejack, who was shaking her head and chuckling. “Ready?”

“Ready as ah’ll ever be,” Applejack said.

The Doctor smiled. A few minutes later, the two Pegasi returned and shut the doors behind them. They had each been given two small cannons that fit over their hooves that allowed them to properly lead the assault. The Doctor set the coordinates and the TARDIS dematerialized, leaving behind a city filled with angry ponies eager on getting their homes back.

Taking Canterlot: part 3

Something has gone wrong. We don't seem to have an archived copy of that chapter.

The Doctor rises

The 6 stood over the Doctor’s lifeless body. For a split second, Twilight didn’t see him coming. She was facing against Chrysalis when Sombra attacked. If he didn’t do anything, Twilight would be dead for real, and Equestria would fall for good. He had told them of the plan, but she didn’t expect him to jump in front of her like that.

This pony is insane! Twilight thought to herself.

Sombra, on the other hoof, was trying so hard to resist finishing all 6 off at once. While he was eager to regain control, he wanted them to accept what happened to the Doctor. Might as well break their spirits before they were obliterated.

Chrysalis still had fear in her eyes, but she was not focused on the lifeless Doctor. Her focus was on the blue box in front of her. She recognized it from a painting back in the Badlands. It hung from Chrysalis’s lair where she would stare for hours, wondering why she was fearful.

A pony born of flames destroyed our once great empire. He wore an endless mask and lived in a blue temple. Whosoever angered this pony, he would simply step from his temple and the earth would shake, she had read in the myths.

Discord looked upon the 6 with concern. His plan called for separating the Elements of Harmony and a clean takeover. He didn’t plan for death and destruction. While he was chaos, even he had guidelines when it came to something like this.

Twilight and Rainbow looked up. “YOU MONSTERS!” Rainbow bellowed out.

Sombra smiled. “A pawn that needs to be taken in the game. I have you in Checkmate, Princess Twilight. You cannot fight, not without the Elements of Harmony. Submit to us, and you all will not share your friend’s fate.”

The 6 looked at each other. Instead of backing down, the 6 stood together behind the Doctor. Sombra smiled. “Then I guess we will be legend after all. Behold, Discord. Tonight, the Elements die!”

Sombra charged his horn, ready to deliver a magical blast. Chrysalis, no longer in a state of fear, charged at the girls.

Twilight smiled as she hit the floor with a spell. The spell created a cloud of pink smoke that enveloped the Changeling Queen.

“Chrysalis, how dare you act without reason!”

The smoke cleared, leaving a very confused Changeling inside. Chrysalis looked around, not seeing any of the ponies who stood before her.
A loud cry echoed from the walls. Chrysalis looked up to see Rainbow charging at her. Chrysalis flew backwards as Rainbow crashed into the floor. Once she was out of the way, Discord sighed as he summoned king cobras from the floor. They slithered toward the cyan pegasus.

A yellow blur flew from nowhere and stood between the snakes and Rainbow Dash. Fluttershy stood strong as her eyes widened into the Stare. The snakes hissed at her and crouched for a strike.

The cobras lunged for the kill.

Fluttershy didn’t move, but the shadow of a horrible deviled monster appeared behind her. The snakes changed direction in midair and slithered away to the stained glassed windows. Discord sighed.

Chrysalis lunged for an attack. Before she got close to Rainbow, a mannequin appeared and stopped Chrysalis. The Changeling Queen sat on her haunches as more mannequins appeared and circled her. They marched in perfect harmony with each other.

Sombra cursed to himself. He fired a half-finished spell at the mannequins, but when one fell, two more appeared. Sombra looked around to see Rarity in the corner with her magic aura at work.

The King of Shadows growled as his pony body turned into black smoke and flew toward the fashionista. He opened his jaws, ready to deliver a killing bite.

“YEEE HAWW!”

A lasso appeared from behind the TARDIS and looped around Sombra’s neck. With his momentum aiding her, Applejack swung Sombra around, narrowly missing Rarity, and into the crowd of mannequins. The dolls were sent flying in all directions, leaving Sombra and Chrysalis in a tangled mess.

Meanwhile, Discord was at a standstill with Pinkie Pie. Whenever the Lord of Chaos summoned either moving piles of apples or cursed cakes, Pinkie simply fired at them with her Party Cannon. The deviled cakes splattered around the room with each explosion. Discord voiced his frustration as he snapped his claw, turning the cannon into a giant log.

Pinkie cried out by the surprise, but it lasted for a second. The party mare pulled deflated balloons from her mane and immediately began to blow. As the balloons got bigger, they got rounder and goldener.

Discord’s jaw hit the floor (no, seriously) as Pinkie held five golden cannon balls. Using her Earth Pony strength, she hurled each cannon ball at the Draconiquus. His slim body enabled him to dodge, but the aftermath was about as crazy as his ‘glass of chocolate milk’ gag. One cannon ball was close enough for Discord to lose his concentration for a second.

Twilight flashed in front of Pinkie and fired a spell at him. He flew through the air and landed near the throne. A second later, two more magic blasts sent Sombra and Chrysalis to his side.

Sombra immediately picked himself up. “You will not take our empire! Not again!”

Sombra’s horn emitted green electric arcs. Before he could fire the spell, Discord cried out. They all looked back at him. His snake-like form was spasming like he was getting the chills. His eyes glowed gold before he managed to calm himself. Sombra looked at him with concern. “What is the matter?”

“I don’t understand. There is a great magical disturbance in two different places happening at the same time. One in the Element Tower, and the other—”

“Where?”

Discord looked up at the lifeless Time Lord. “There.”

Everypony turned their eyes to the Doctor. Without warning, the ceiling caved in. Falling from the sky was Princess Luna. She was littered with minor cuts and bruises, but she was alive. Appearing next to Sombra was Nightmare, who was missing her helmet. She was scrapped in several places, especially around the face, but she was in better condition than Luna. “They entered the Element Tower. We have our children holding it against the pegasus intruder. She will not get the Elements. Now, what is the problem here?”

Sombra sighed. “Discord has sensed a magical disturbance where the brown pony lies. He is dead, Discord! There cannot be a magical field around him,” he said as he glared at the draconiquus.

“But I am serious about this. I’m picking up a surge of energy coming from that Doctor guy,” he said.

Chrysalis smiled. “You are probably picking up his soul leaving this world. There is no way that he—”

A struggled groan broke Chrysalis’s thought. The 4 looked over, and picking himself off from the ground was the Doctor. As he rose, a look of disbelief formed on Twilight. He took a serious magic curse for her that should’ve killed him. Once he was on all four of his hooves, he brushed off his forelegs like he rolled in the dirt. In the center of his chest was a burn mark.

Sombra was in disbelief as well. “But-but that was my most powerful spell. It’s supposed to be powerful enough to put down an alicorn!”

“Then I have a lot of questions for you, but first I must say: by all the stars in the sky did that hurt! I’ve felt a lot of pain in my days, but that hurt beyond everything else. Mainly because I’ve managed to cheat death for about 30 years or so. Yeah, that will take a lot more energy than I would’ve wanted to use.” He turned to the 6. “You all OK?”

All the ponies nodded their heads. “Sorry for scaring you like that, but if I mentioned doing that, you all would’ve tried to stop me. This is the only way I can help,” he said.

Twilight shook her head. “That was the most reckless thing I’ve ever seen!”

“Darling, you have a serious mark on you from that magic blast,” Rarity pointed out.

He smiled. “Want to see a magic trick?”

The Doctor took a deep breath. He moved his hoof over the mark, and as it brushed over his fur, the mark disappeared. He took a deep breath as he calmed his hearts. “Feel better now?”

The 6 said nothing. He shrugged to turn back to Sombra. His horn was charged once again. “How did you do that? You’re just a regular pony!”

The Doctor turned to the TARDIS. “Can regular ponies pilot the TARDIS? Can a regular pony have dashing good looks like me?” The Doctor smiled for emphasis. “No, I am not a regular pony! Regular is boring!”

Chrysalis looked on in fear. “That box, what is it?”

“It’s called the TARDIS. It stands for Time and Relative Dimension in Space. It can travel anywhere in time and space, and it’s mine,” he said.

Applejack looked back at the TARDIS. Time machine?

Nightmare laughed. “Time machine? That is impossible, even with magic. Starswirl only completed one small spell to travel in time and that only works for a short amount of time. It is impossible.”

“Nothing is impossible, just difficult to complete.”

The Doctor fixed his stance. “I just find this all amusing that you have gone through all this just to be stopped by six ponies,” the Doctor said.

Nightmare laughed. “Us? We overpower those puny ponies. Separate, we don’t stand a chance against you all, but now with our assembled powers, you six will be destroyed!”

The Doctor smiled. “That is all I needed to hear. You threatening to destroy them, my friends, will not sit kindly with me. You don’t want to see me when I am determined to keep the ponies I care about safe. You have no idea what you are getting yourself into,” he said.

Sombra smiled. “You are trying to sound brave, but I smell fear on you. As the master in the art, I can sense if ponies have a particular fear. You have monsters you don’t want to resurface. 10 monsters are rising, Doctor, and I will gladly work with them to ensure that you will never raise your head again!”

Sombra reached out with his magic, grabbing all the minds of everypony in the room. Discord, feeling left out, pulled a wire out of thin air and plugging into Nightmare’s horn. The alicorn gave him an odd look as he shrugged it off. Even the Mane 6 was plugged into Sombra’s mind. The unicorn approached the Doctor, who was standing tall. “Let’s see what this Doctor fears, shall we?”

The rest of the 4 agreed. Sombra’s horn touched the Doctor’s forehead and the room was engulfed in a green light.

Instead of one pony screaming, there were 4 screams. Sombra and the rest of the 4 screamed in terror as the visions entered their minds. In them was a tall, hairless ape in a long brown coat. His mane was small and ruffled, but his eyes. Oh, his eyes burned with a great fire.

The visions showed at least one of the creatures, but they all were different. One wore a strange brown hat and scarf, another wore a white jacket with a celery stalk pinned on it. One wore a leather jacket and held a silver stick with a blue light. With a press of a button, the vision changed once more.

The Doctor forced the last image into his mind. It was the image of a tall man with a brown suit and jacket. He had spiky hair and he was the Doctor. He stood in front of an army of various creatures, all appeared to be in metal. Giant creatures in suits of armor, mysterious egg-like creatures with eyestalks, and many more monsters. Some were red with suction cups, others were slimy. Some were fat and…gassy. For a moment, Sombra thought he saw potatoes with big black plastic wands.

“I am not just a regular pony! Entire armies have turned and ran away at the mention of my name!”

The Doctor in the image took one step forward, and the army of monsters immediately turned and ran. Some tried to fight back, but the Doctor would not fall. So many of the creatures fired what appeared to be magical blasts at the Doctor, but he simply dodged them. Raising his screwdriver, the Doctor pressed the button. The remaining monsters turned to ash and dust.

“I am the survivor, nay, the winner of the last great Time War! I watched two almighty races burn and turn to dust! I have topples gods, raised empires, and burned stars with the words of my people! You are nothing compared to me!”

An image of a planet entered their minds. The planet burst into flames. The scene was enlarged and a vision of an elder man appeared to be shooting fire from his hands and face. As the fires rages, the man let out a blood-curdling scream. Entire structures fell and the egg-like creatures seen before were screaming in pain as the fires rages.

Twilight couldn’t believe what she was seeing. The Doctor was endless. His power in this new form seemed to surpass his power now. “I will not stand idle while you destroy this world. As the last of my species, I will never allow you to win!”

The vision died in everypony’s minds. Sombra looked up, and the Doctor was starting to emit golden smoke from his hooves. “But-but you still don’t have the Elements. We are still more powerful!”

Right as he said that, they heard a mare call his name. “DOCTOR!”

The 4 looked for the mare. It was Ditzy with a chest full of the Elements. Ditzy dropped the box off in front of Twilight, who gladly opened it. “Sorry Sombra, but it looks like this is Checkmate,” she said as she grabbed each of the necklaces.

“Time to get this party started!” cheered Pinkie as her Element was placed on her.

“YEEEE HAWWW!” cheered Applejack.

“Yay!” Fluttershy cheered.

“Well it’s about to get beyond 20% cooler,” Rainbow Dash said.

“This has gone on far enough,” Rarity said.

With all the Mane 6 with their Elements, Twilight’s crown began to glow along with the others. The five Elements started to emit magic to Twilight’s. The cracks on the jewel began to disappear in front of the 4, who were now struck with fear. The Element of Magic was now fully healed.

Sombra shook his head. “What are you?”

“I am not just a pony. I am a Time Lord! I am the Doctor! I am 904 years old! I come from the planet Gallifrey in the constellation of Kasterborous. I am the Oncoming Storm, the Bringer of Darkness and your worst nightmare! Now it is time to say goodnight Sombra.”

The smoke completely engulfed the Doctor. His brown coat began to glow gold. “Well then, ALLONS-Y!”

With a swift motion, the Doctor rose on his hind legs. His entire body erupted into flames as Sombra screamed. Twilight started to feel the magic of the Elements take over.

“Ready girls?”

“READY” the girls said in unison.

With her friends behind her, she was ready. The girls all raised up into the air as their Elements charged. The 5 fired beams of concentrated magic at Twilight, who fired them at the Doctor. The flames of his regeneration started to move toward the 4, who were paralyzed in fear. The flames engulfed the 4, and the screams of the former rulers of Equestria echoed through the halls.

Sombra was first. He looked down at his hooves, and he noticed that they were cracking like glass. Before he could say another word, his entire body exploded and reformed. His horn, the only thing that remained flew toward the ground. The broken pieces of the King of Fear began to turn into stone around his horn. The pieces created a stone pedestal and an octagon piece with Sombra’s horn in the middle.

Discord screamed as he felt his form cracked, but as he was about to explode, he felt time stop around him. The flames no longer burned his skin. The world became silent. The draconiquus looked around, wondering why the world became silent and still. Out of the corner of his eye, he spotted a pony wearing a giant blue hat and cape. His coat was white and he had a long beard that touched the ground.

Not here, Discord. Your destiny doesn’t end here. You are required for much bigger events. Escape now! The pony commanded.

Without arguing, Discord vanished into thin air. The pony in white fired a magical spell into the air, hitting everypony on the planet. Once the spell was performed, he vanished, restarting time. The flames continued to rage around Nightmare and Chrysalis.

Chrysalis turned to Nightmare. “You promised me victory, Nightmare Moon! You promised!”

Chrysalis’ form cracked and exploded. For her mark, the image of a chrysalis took the center of the octagonal stone piece. The statue was near completion.

Nightmare screamed before her last words echoed through the halls. “YOU WILL ALL PAY FOR THIS! I AM NEVER TRULY DEFEATED! EVERY DREAM HAS A NIGHTMARE!”

With those last words, Nightmare Moon’s form cracked and exploded. The crescent moon, representing her cutie mark, flew into the statue as the third and final octagonal piece built around it. The statue consisted of the three symbols of those who were defeated. Once the flames of the Doctor’s regeneration died down, the Time Lord crumpled to the floor. He was the same as he was before the regeneration. His coat still that chocolate brown that he grew accustomed to.

Twilight smiled as the Elements finished the job, but it wasn’t over. The world was still shrouded in eternal darkness. With the power still running through their veins, the Mane 6 burst through the ceiling and straight into the sky. Their charged forms left a trail of magic behind them.

The Doctor awoke from his regeneration. Without a second to assess the situation, he turned to his earpiece that he kept hidden. “Cadence, Shining Armor, do it!”

In the Crystal Empire, the royal couple had a group of ponies surround the Crystal Heart. Pouring their magic and love into it, the Heart began to awaken once again. It spun at a rapid pace, and with Cadence’s last bit of magic, the Heart exploded with magic, shooting a ray of magic into the sky. The beam diverted toward Canterlot in the south.

The Mane 6 saw the beam from the Crystal Heart coming toward them. Focusing their magic into the spell, both the Mane 6 and the magic beam collided and lit up the sky in the biggest Sonic Rainboom in existence. The explosion rocked all of Equestria at the same time.

In Canterlot, Trixie and the main cellist, Octavia Melody held back the Changelings and Shadow Ponies. When the explosion came above them, everypony stopped fighting. "EVERYPONY GET DOWN!"

The Rainboom ran above the city, and behind the initial explosion, the sky cracked. Behind what appeared to be the magical barrier was sunlight. A Shadow Pony happened to be standing when the light hit it. The Shadow Pony screeched in pain as it evaporated into thin air.

All the Shadow Ponies went into panic mode. They all attempted to escape the sunlight, but the sky was cracking faster than they were running. Shadow Ponies by the millions around Equestria began to evaporate due to the sunlight. Changelings also managed to escape, some turning into regular ponies to escape prosecution from whatever was going to hunt them down.

As the sun shined throughout the land, the Doctor and Ditzy smiled. With the sun hitting his face, the Doctor shut his eyes. Exhaustion swept over him as he fell asleep.

The storm was over.

Aftermath of the war

The sound of the Doctor’s Sonic Screwdriver and intense headache jolted her from her sleep.

The last thing Rainbow Dash remembered was the Doctor shooting golden flames from his body and Twilight charging the Elements. Once again, incredible power surged through the cyan pegasus as Twilight fired the one spell the Doctor told her to conjure: the Reversal Spell. While she didn’t care so much about magic, Rainbow found herself grabbed by the Doctor’s plan to take down the Shadow Trio. While he left behind the detail that he had to die, the plan was Rainbow Dash approved.

The cyan pegasus slowly opened her eyes. She was in the throne room of the castle. The stained glass windows were all shattered, there were three burn marks in the floor, and standing close to the throne itself was a small statue. The statue was divided into three parts, each represented by an octagon. Next to the statue was the Doctor with his Screwdriver in his mouth and Ditzy next to him. They both looked like they were studying the statue.

RD tried to rise to her hooves, but her body felt like lead. Her wings were tired from doing something. She wasn’t flying in her sleep again, right?

Before she gave up and fell back asleep, she felt an aura of magical energy engulf her. She found herself rising to her hooves and her energy restored. In front of her was Twilight, who looked beaten up as well. She had scratches covering her entire body and bags under her eyes. “Good thing you’re awake,” Twilight said.

Rainbow smiled. “You interrupted my nap, but seeing that we beat those jokers, I say I forgive you,” the pegasus joked.

Twilight laughed and they hoofed. “Are the others awake?”

“Yeah, but they’ve been awake for a while. It took a while to wake you up though. I didn’t know your coat turns white when you get too tired,” the alicorn said.

Rainbow froze. “White? My coat is blue, not white!”

“But it was—nevermind. I don’t want to know. Next thing I know, I’m asking Pinkie why she has wings under her coat.”

The two friends laughed, but stopped. They both looked over to Pinkie, who was bugging Luna about wanting to see the castle on the Moon. RD had to do a double take because she remembered Luna crashing through the ceiling thanks to Nightmare Moon. She was laughing when Pinkie started showing her the signature Party Cannon. Wait until Pinkie wants to fire it.

“12!” they heard the Doctor said.

Both ponies turned to the Time Lord. “What?”

“Time locks. 12 Time Locks are in place inside the statue. I didn’t think about Time Locks being implemented but it got the job done,” he said. “Oh, and welcome back to the world of the living. I didn’t expect you to take charge of the Rainboom like that Ms. Dash. That was amazing to watch.”

“Huh?”

Twilight smiled. “I was awake for it. We shot straight up into the air and did the biggest Sonic Rainboom I’ve ever seen. It broke through Nightmare’s spell like that baseball when it broke through my kitchen window,” she said with a glare at RD.

“Can you quit bringing it up?”

The princess of magic shook her head. “Anyway, I got Spike to get Princess Celestia. Hopefully he didn’t get lost.”

“Are you sure the poor darling isn’t still at the doors wondering why it’s bigger on the inside?” Rarity asked.

“Ah’m still trying to figure it out mahself,” Applejack said.

Rarity agreed. Twilight looked back at the TARDIS. Perhaps her little dragon was still in shock from it all.

The doors suddenly opened. Spike was walking out with Princess Celestia behind him. She looked weary and most of her horn was still broken. It was better than before, but magic was still off limits for the alicorn princess. Before she moved her hoof, Luna was already running to her sister. She embraced her sister in the biggest bear hug in the history of bear hugs. Celestia’s yelp of pain and surprise didn’t stop Luna from squeezing.

Twilight smiled. She was going to have to find Cadence and Shining Armor and do the same thing. Maybe it can be a family night. Or brunch. Maybe a late lunch/early dinner thing.

The alicorn shook the idea out of her head. Maybe later.

The Doctor walked up to the princesses. “I think Celestia wants to breathe sometime soon,” he said.

Luna sighed and let her sister go. She mocked suffocating and gasping for air for the amusement of the ponies of the room. “Oh Doctor, the legends are very true. You do leave a mess wherever you go,” Celestia said as she surveyed the room.

The Time Lord chuckled. “Wasn’t me this time, or was it? No, I was regenerating. Oh, and be careful with that statue over there, it has the three fake gods in there,” he said.

The princess of the Sun looked at the statue. “Why am I not surprised?”

Pinkie jumped up. “Because you know the Doctor?”

“Just about right, little one. Well, there is a lot of cleaning up to do. Why don’t you take the statue to the catacombs of the castle, Doctor? We can clean this place up.”

The Time Lord nodded. “Ditzy, help with the clean up.”

“Okie-dokie,” she said.

The Doctor grabbed the statue with his mouth and walked out of the throne room. Celestia sighed. “Where’s Discord? He needs to help with the clean up.”

Fluttershy smiled. “I’ll go get him.”

“No, he should come here. There is no telling where that draconiquus is hiding. Discord!”

In a flash of light, a small box appeared in the middle of the room. The box started to play a song, and when it ended, Discord sprung out like the joker in a Jack-in-the-Box. He wore a jester hat and held a flower as a staff. Celestia shook her head.

“Somepony call my name?”

“Yes. We need you to help with the community to rebuild. I’m not sure if you heard, but Sombra tried to take over Equestria with Nightmare Moon and Chrysalis.”

In the back of Discord’s mind, a red alert flashed. They don’t remember me!

The box disappeared and Discord reappeared with a reflecting jacket and hard hat. “Just don’t let the pink one near any power tools and you got yourself a deal.”

Twilight looked up. “Power tools?”

The draconiquus waved it off. He glared at the TARDIS. That Time Lord and his box ruined his plans again. Without another thought, he disappeared to probably begin the reconstruction. Either that, or he was going to take a nap. Twilight shook her head. “Who knows what he was doing while Sombra was here?”

None of the ponies answered. “Maybe he was trying to fight him off?” Fluttershy said.

“I’m sorry darling, but isn’t Discord stronger?” Rarity asked.

Celestia nodded. “We shouldn’t focus on Discord right now. Twilight, I want you to properly secure the Elements. Sister, I’m going to need some rest and hopefully I can heal faster. Can you take my place—”

“We can gladly take thy place in supervising the clean-up and help with the reconstruction,” she said.

Celestia chuckled. “No Luna. Reconstruction will take probably a few weeks, and we must also be ready for the Summer Sun Celebration coming up. I am asking you if you can carry on my duties as Princess of the Sun and the Moon until I recover.

The Princess of the Night was stunned. “Uh, yes. Yes! I humbly accept!”

“Very well Luna.”

The girls all cheered and ran out of the throne room to start with the clean-up.

It felt like weeks since the endless night ended and the clean-up began. Ponies all over were cleaning up the propaganda and banners left behind during what the Doctor called ‘The Shadow Rebellion’. The statue was placed in a high-security chamber deep underground. The room itself was sealed in magic and a Time Lock, making it impossible for the three to escape. Discord could never find his three fallen comrades and gave up on the plan altogether. Nothing was going to happen with the Doctor around.

Speaking of the Doctor, the Time Lord and his companion stuck around and treated Celestia while she was healing. With some more Time Lord sciences and medicines, her horn almost completely grew back. The exposure of her Magic Core, observed by the Doctor, was no longer a threat, but her magic was weak. She would need more time to regain her lost energy. That didn’t stop Luna from taking control of the Sun and Moon while she was ill.

Finally, after a month of working cross Equestria, Canterlot was back to being the shining jewel of Equestria. Princess Cadence reported that the Crystal Empire was back at full power and the Crystal Heart was shining bright. Ponyville and many cities were shining bright thanks to the leadership of the Mane 6. It was so great in fact that the Equestria Games were to continue in the Empire.

On a bright Saturday afternoon, exactly a month since the end of Sombra’s brief reign, Canterlot was busy. Princess Celestia had called for a celebration to honor the heroes who defeated the royals of the Shadow Rebellion. The celebration was to be held in Canterlot castle with Cadence and Shining Armor attending. The whole city was the center of the world.

Inside Canterlot castle, Princess Celestia and Luna stood in front of a crowd of hundreds of ponies. Outside in the gardens, thousands upon thousands of ponies were ready for a whole 24 hours of celebrating. The Galaxy Watch that was put off would be one of the many night-time celebrations. Luna was elated.

The crowd of ponies fell silent as the trumpets blared, calling for their attention. Princess Celestia and Luna extended their wings.

“Fillies and Gentlecolts, I am glad that you all could attend. Today, we honor the ponies who fought against the world’s worst demons to ensure that we live in peace. Today, our heroes will be rewarded for their efforts. Please join us as we welcome our heroes: Twilight Sparkle, Rainbow Dash, Applejack, Rarity, Fluttershy, Pinkie Pie, Ditzy Do and the Doctor!”

As their names rang through the halls, the doors came open and the 8 ponies came walking out. Ditzy and the Doctor smiled as they greeted the crowd of ponies, but the Doctor knew that this wasn’t meant for him. All he did was drive the heroes around and sacrificed himself to correctly perform the spell that saved Equestria. It wasn’t him.

Twilight felt her soul lift up. It felt good to finally celebrate after a month of working to rebuild. She looked over at her friends and took a mental note to never forget just how powerful they were when they were united.

Unity through Harmony? Hmm… Twilight thought.

The lavender alicorn found herself staring at Applejack. She told the truth concerning her new status as a princess of Equestria, yet she acted like nothing was bothering her. She was going to have a talk with Applejack later to discuss the problem.

They approached the steps to Celestia and Luna’s thrones. They both looked proud. “These ponies have demonstrated feats of great strength during the darkest days of our history. The proved to us that if we set our sights on a particular goal, and we work hard, we can accomplish anything.”

Celestia magically produced a small chest. Inside was 9 golden medals. She placed all the medals onto the ponies before her. Even Ditzy and the Doctor received medals for their involvement. Once the medals were distributed, Luna looked back in the chest.

She turned to Celestia. “Sister, there is one more medal in the chest,” she whispered.

The elder sister smiled. “I know.”

She turned to the crowd. “While these 8 ponies worked on the front lines, I cannot overlook one more hero. This hero risked her own safety multiple times to ensure that her friends get their work done. Without her, Twilight Sparkle and her friends would not be here today and the Sun would not be shining.”

She raised the 9th medal. “I take great pride in bestowing this medal on my sister, Princess Luna.”

Luna turned in shock to her sister. Celestia smiled at her young sister. “While I was healing, it was my sister who stuck by me and ensured that my health would worry her less. It was also because of her that Twilight Sparkle is here. She saved her life, and that is great itself.”

She pinned the medal onto her sister. “My sister has kept Equestria in balance and maintained power. I am very proud of her.”

Twilight smiled. “Behold, citizens of Equestria, your heroes are here!”

The ponies started to cheer. Luna smiled as she looked down at her medal. She had something material to be proud of. The Doctor and Ditzy cheered for their friends and their accomplishments. The Doctor kept a note in his mind saying he should check up on the 6 in the future.

All the cheering ceased immediately. The noise in the room was replaced by the sound of cloister bells. The Doctor immediately recognized that sound. He slowly turned back to the doors, and under the archway was the TARDIS. The doors were wide open and the interior was blanketed in a red light. All the ponies in the room began muttering amongst themselves. Celestia and Luna were shocked at the time machine’s sudden interest to join the celebration.

Ditzy, on the other hoof was more interested in the stained glass windows above the two princesses. “Doctor?”

The Time Lord turned around to face the windows. With one glance, he gasped. Written on the windows were the two words he dreaded to see: BAD WOLF. The words were written in red. Everywhere he turned, the same two words rang in his head. Ponies started to freak out at the sudden appearance of the words. Some got the idea it was written in blood.

The Doctor’s two hearts started to beat faster as he processed the words. The hairs on the back of his neck stood up as more ponies started to freak out. One pony screamed louder than everypony else. “There’s a wolf in here!”

The Doctor turned around, and standing in front of the TARDIS was the Bad Wolf itself. The wolf was sandy-colored with golden eyes. It sat patiently in front of the TARDIS. Hello Doctor, long time no see.

Return of the Time Lord

The wolf sat in front of the TARDIS, taunting the Doctor. She was licking her paw and flicking her tail around, frightening the ponies around her. Celestia and Luna were frozen in fear, but the Doctor was as calm as he could be. He walked down the carpet from the throne to the wolf’s face. She stopped licking her paw and flicked her tail. The cloister bells inside the TARDIS ceased and the red light faded. The doors closed and the Doctor smiled. “BAD WOLF.”

Doctor, it is good to see you once again. My my, it has been a while, she said.

“Yes, I remember. The Time War above the Earth was the last time, wasn’t it?”

I remember Davros’s attempted destruction of the Multi-verse. Those were the good days though, weren’t they?

The Doctor grimaced. “I don’t like to remember and I highly doubt they were good times."

The BAD WOLF smiled. You don’t have a choice.

Behind him, Princess Celestia screamed out. “GUARDS!”

Behind the TARDIS, armored Pegasi and Unicorns charged at the BAD WOLF with spears. Earth Pony guards appeared from the two exists near the thrones and charged with armored helmets. The Doctor looked around with eyes wide. “No, DON’T!”

It was too late. Once the armed ponies got close, the BAD WOLF’s eyes glowed gold and their spears turned to snakes. The armed ponies dropped the snakes immediately. The Earth Pony guards’ helmets turned into pillows. They hit the BAD WOLF, but the only thing that happened was the room being filled with pillows. Twilight’s jaw hung by the display of magic. The wolf’s magic originated from her eyes, not the horn.

The wolf smiled. Looks like my powers still work in this Universe. Fantastic, she said.

The Doctor sighed. “Why are you here?”

I’m just passing through. I have to return to your Universe to gather the last component to the problem at hand. Although, I’m sure I can obtain what I need here.

It took the Doctor a moment to think about it. His eyes widened. “You don’t mean—”

The Doctor must return to the Universe. We need you Doctor.

The Doctor laughed. “Oh no. No way is that happening. I’m no longer needed in that Universe. I regenerated. My future self is running around in that Universe—”

And he needs your help.

Celestia’s heart quickened. There is a fluxuation in time. An event that can still go in any direction. An event you want to repeat and this time, you have a third choice.

The room was silent. Gallifrey.

The fires in the Doctor’s eyes raged. Ditzy walked over to the Doctor with concern in her eyes. “Doctor? Are you alright?”

He said nothing. “Doctor? Please say you’re alright.”

“But it’s gone. I destroyed Gallifrey in order to stop the Time War. There cannot be a fluxuation in that particular event. It’s a part of my time stream. Interfering in the Time War again would result in me crossing my own time stream. I cannot do that, unless I want the Universe to burn. Besides, there can’t be a third choice,” he said with a cracked voice.

Ah, but that is the beauty of being the only Time Lord in existence. It is your words that define the laws of Time and Space. You can cross your own time stream by your word.

“No I can’t! Besides, if I could, the war is Time Locked. I won’t be able to intervene due to my people’s own decision to lock the war. I cannot break the lock.”

The BAD WOLF smiled. It can be done. I’ve seen it. Gallifrey escaped the Time Lock before, thanks to Lord President and the Master. The Lock was broken by you when you decided to join the fighting. The Lock can be broken.

“But I can’t do it alone! I had help, I had resources!”

The wolf’s eyes glowed. Dear Doctor, you regret the decision you made all those years ago, don’t you?

The Time Lord sighed and nodded. Then you know that somewhere deep down, you had a way to escape it. Either the Universe burns or Gallifrey falls. It is decisions like this that haunt many people and ponies. Princess Celestia faced that fact when Nightmare rose from the dark.

Celestia bowed her head in sadness. You faced this decision on Gallifrey, and you chose the same choice Celestia made. For the good of the masses, you chose to cut your heart out. Now, you have a chance to heal. I can send you back to Gallifrey. You can save it. Gallifrey falls no more.

Those words rang out to those who understood what the BAD WOLF was talking about. Twilight’s heart pretty much stopped. If what the wolf was saying is true, then the Doctor can heal from his pain. When he talked about crossing his own time stream, however, it made her think back to when she used Starswirl’s Time Spell to tell herself not to worry about the following week (which failed). Perhaps telling that to the Doctor would be a bad idea.

Celestia looked over at her sister, who was taking in what the wolf was talking about. Celestia really did have no other choice but to banish Nightmare to the moon, even if she lost her sister in the process. She went over and hugged the princess of the Moon, who returned the display of kindness.

The wolf breathed in. If you wish to save Gallifrey, then you will come with me. While you may accept, I must warn you that you cannot fly off still in a pony body.

The Doctor laughed. He would meet his future incarnation as a pony while the other would question his sanity, again. “You have a point there. I suppose I can go back and change everything.”

I am happy you made that decision. With that, the BAD WOLF smiled and her eyes started to glow once again. This time, the Doctor’s body began to glow like he was regenerating. The flames erupted, but they were gentle this time. The Mane 6 shielded themselves from the fires of the Doctor’s transformation.

The flames died down, and in front of the whole of Equestria was not the same brown stallion as before. The creature in front of them was very tall and pink. The creature had enlarged forehooves that had strange digits at the ends of them. His brown fur was replaced by a brown long coat. Underneath the coat was a brown suit and tie with an hourglass tie pin attached to it. The creature’s face was long and narrow. His snout was smaller and his mane was on top of his head. It was still as messy as before.

The creature looked down at the digits before him. He smiled as he reached into his coat and pulled out his Sonic Screwdriver. With a quick buzz at the crowd, the Doctor was back.

Ditzy flew up to the Doctor’s new face. Instead of keeping her space, the pegasus hugged the Time Lord. The Doctor hugged back. “Oh it’s so good to look like a Time Lord again!”

Princess Celestia smiled. “What’s wrong with looking like a pony?”

“Well, I grabbed everything with my teeth and probably contracted several diseases, my fear of appearing everywhere in the buff is gone, and I can now grab things like I did before. Oh it feels so good to be back!” the Doctor said.

The princesses chuckled. The TARDIS grew to accommodate his new size. The BAD WOLF smiled up at the Time Lord. I must say, I missed this form. And now, dear Doctor, it is time. Gallifrey awaits.

The Doctor nodded and kneeled down in front of his friends. “Alright, looks like I’m going away for a little while. Ditzy, take good care of yourself. Celestia, I expect you to be better at chess when I get back, and you Luna—”

He pointed at the alicorn “—we got a rematch coming up. Be ready.”

The princess of the Night smiled. “Fighting is Magic is my territory, dear Doctor. I’m afraid I must ask you to improve your skills.”

The Doctor laughed. “We’ll see.” He turned to the Mane 6. “It’s been a pleasure working with all of you. We made a pretty good team, didn’t we?”

The girls all agreed. Pinkie smiled and wiped a tear from a hanky pulled from Rarity’s dress. “We’ll miss ya Doctor!”

Rarity looked over. “Pinkie, that goes on my dress!”

“Sorry, I’ll put it back.”

“Egh, just keep it. It looked rubbish anyway,” she said.

The Doctor cracked a smile. While Twilight joined in on the little conversation with Rarity, the Doctor eyed Applejack. With a silent nod, the message was clear. Stay strong. The farm pony nodded in a response and looked back at Twilight. She was going to have a rough next few years.

The Doctor turned to the BAD WOLF, who had the doors of the TARDIS opened. I’ve created a pathway to our Universe, Doctor. Once you have completed your mission, you can use the same route to return.

He smiled and walked toward the TARDIS. Just before he entered, he turned around to face his friends again. He chuckled as he looked back up at the TARDIS. “Well then, enjoy the celebration! I remember it well. Oh, and lay off the confetti cannons unless you want the fountain to be filled with surprised ponies.”

That warning was directed at Pinkie Pie. The Doctor smiled. “Well then, Allons-y!”

He closed the doors of the TARDIS. Immediately the engines started to kick up as the wonderful machine began to vanish from the Equestrian throne room. After a few moments, the TARDIS was completely gone, leaving the guards to deal with the snakes that were rudely turned by the BAD WOLF and the graffiti gone from the walls.

The Doctor flipped a few switches on the console as the TARDIS flew safely between dimensions. He couldn’t stop looking at his hands as he worked in his wonderful machine. In his mind, he replayed how he would save Gallifrey and what his future self looked like. If he looks like a dork, he was going to lose it. Well, maybe if he was ginger, he wouldn’t mind as much.

As he continued to work with the TARDIS, the BAD WOLF stood nearby. She raised her paw at the Doctor’s head. You won’t be going directly to Gallifrey.

The Doctor stopped what he was doing. Her Majesty, Queen Elizabeth I needs your help. A group of Zygons have invaded England and are attempting to take control of the planet. You must travel to 1562 and snuff out the Zygons. It is there where your mission begins. You will also have no memory of you ever living in Equestria. Your last memory will be your journey to Mars after Davros’s plot. Best of luck is wished upon you, Doctor.

The BAD WOLF lowered her paw. The Doctor shook his head and continued working at the console. With no more items on her agenda, except one more visit, the BAD WOLF vanished.

A new passenger

Ditzy smiled as the dream returned to her.

She was sitting on top of a cliff, overlooking a magnificent sunrise over an alien planet. The planet she wason was Bermuda 15, the beach planet. The planet is said to have sunrises that could melt the hearts of anypony who watched it. The planet was also the planet where the Doctor helped stop an infestation of the Black Demon virus, a virus that turned ponies into hallow shells of pure evil. Ditzy was lucky to have stumbled across the antidote when the Doctor fell ill.

As the sun rose above the horizon, she could feel the Doctor sitting next to her. “Well, off on another adventure?”

Ditzy sighed as she looked over at him. She didn’t have the familiar shine in her eyes whenever he asked that. In fact, in her eyes was confusion. Not about the question, but about her future as a citizen of a little planet tens of millions of light years away from there. She felt herself slip off the cliff and into the water. The Doctor shrieked and jumped in after her.

Ditzy felt herself sink to the bottom. She saw the Doctor break into the surface of the ocean and saw him swim to her. He was inches away from her hoof when she knocked it away. His hoof turned into smoke as his image faded into the water. The ocean was weighing down on Ditzy’s chest, but she welcomed the pain. She felt herself softly land on the ocean floor. The darkness had enveloped her completely. She felt the eyes of sea creatures around her.

The wall-eyed pegasus looked around at her surroundings. Indeed, sea creatures of every size and species came to see her. Some looked fearsome while others looked at her with confusion. One of the sea creatures approached her with hesitation. She held her arms out as the creature came between them. They both shared a hug under the sea.

Ditzy’s eyes shot open. Her eyes readjusted as she looked around her. She felt her breathing labored and her chest heavy. She was on her bed and in her room. It was night with a full moon. Ever since the Doctor disappeared, Ponyville had its share of unusual happenings. The Everfree Forest attacked the city and the bearers of the Elements were powerless. The Forest had retreated, but the Mane 6 returned with no jewels.

When the trials for the Equestria Games came in, she was put on the Ponyville team to replace Rainbow Dash while she was injured. Of course, she immediately recovered, but she didn’t mind. She was still there when the games began. The peaceful scene of Equestria had ceased after the sudden attack against the princesses a while ago. Ever since then, it had been one chaotic thing after another.

Ditzy’s ear twitched at a faint sound growing in the distance. She hopped out of her bed and ran to the window. There was the magical blue box that she remembered so well. She quickly flew down the stairs and threw up the door. Of course, there was the Doctor with his blue suit vest and tie. He didn’t look a day older than when he left. His usual grin greeted the pegasus. “Doctor, you’re back!”

“And it’s good to be back. I’ve got to say, it took me a while to get the hang of my hands and feet again,” he said.

“You mean those weird things that other weird thing gave you?”

He nodded and chuckled. “Anyway, I’m back for you. We still have a whole Universe to explore, and more bad guys to stop. What do you say, wanna come back to the TARDIS?”

Ditzy’s face began to burn up with embarrassment. The Doctor was quick to notice. With no more words, she walked into the house and motioned the Doctor to follow.

The Doctor sighed as he entered the room. The room was just big enough for a filly, and sure enough, there was a young unicorn sleeping in the bed. An old music box was playing in the background, probably what lulled the filly to sleep in the first place. The Doctor wanted to curl up and sleep as well with the music playing, but he knew that wasn’t going to happen.

“How long was I gone?”

“3 and a half years Doctor. I found her a while ago and Carrot Top helped me raise her. I wanna be there for her Doctor, so I am retiring from the TARDIS,” Ditzy said.

The Doctor smiled. “You remind me of the nanny we met on Mal-Relati. I understand Derpy, and I imagine that these past few months have been tough on you,” he said.

Ditzy nodded. “So many things happened Doctor, but I want Dinky to be safe.”

“Oh so her name is Dinky?”

Ditzy smiled. She yawned as she closed the door. “I wanna get some sleep Doctor. You don’t mind, do you?”

The Doctor only smiled. “Has my derpy best friend finally grown up?”

She smiled and shook her head. “Nope, I’m still me. I accidentally almost crashed into Rainbow Dash’s house the other day. I ended up crashing into Twilight’s castle though, but she wasn’t home,” she said.

The Doctor sighed and gave his Derpy companion a pat on the head. "Take care of yourself Ditzy."

"You too Doc."

The Doctor waved goodbye to Ditzy as left the house, leaving Ditzy to her daughter’s bedroom door. As she turned in the opposite direction of the Doctor, she could hear the sound of the engines firing up. She shut her eyes and focused on the sound of the TARDIS. She implanted the sound into her memory before heading back into bed. That would be the last time she would be inside the TARDIS. She didn’t count on the fact that she would see the Doctor again, but it would be under a different set of circumstances. Circumstances that would bring the Doctor back from the end of time.

Applejack was sound asleep when she heard the TARDIS engines.

Even though it had been two and a half years since Tirek unleashed pure chaos in Equestria, Applejack still had nightmares from that day. She would scream at night, trying to fight off Tirek as she tried sucking every ounce of her life force away. Her nightmares always started after Twilight surrendered to the demonic centaur. Discord would still be trapped and without the last key, they were doomed. Applejack remembered that day, and the events following it.

Apple Bloom and her friends were lucky to have been camping with Zecora when Tirek was free. Fearing their safety, Applejack sent the CMC away in order to deal with the problem. Her plan worked, and telling her young sister about what had happened was bad enough.

She was in the middle of the field, and Tirek hoisted her up to his eye level. Applejack was petrified, and right as he began extracting her life force, the sounds of a whirring engine erupted. The dream Tirek and Applejack turned to the sound of the noise. Materializing on the field was a small blue box. Tirek released Applejack and approached the box. A brown stallion emerged from the box and calmly walked up to the cloven hoof of Tirek.

The stallion looked up and chuckled. “I’ve seen worse than you! Ponies have nightmares of you, but you will soon be having nightmares of me!” he said.

Applejack smiled. She looked up and noticed a hole burning in Tirek’s chest as the stallion continued to stare into his soul. An explosion erupted behind her, and she saw herself and the rest of the Mane 6 with their new magical forms. They cast a spell on Tirek, destroying his power. Applejack smiled as she remembered that moment.

The cowpony ran to the Doctor and threw a big hug on him. He chuckled and returned the hug. Before she could say anything, the Doctor whispered in her ear: “Wake up.”

Applejack sat straight up in her bed. She looked around her room. Nopony was there. She wiped the sweat off her forehead and proceeded back to sleep, but she heard the sounds of a rusty, whirring machine coming from outside. She recognized that sound immediately. She looked out her window. Outside the farm, the Doctor’s TARDIS was materializing at the edge of the Everfree. She smiled as she grabbed her Stetson and bolted out the door.

She snuck out of the barnhouse and ran through the fields. When she reached the border between her farm and the Everfree Forest, she stopped. It was really the TARDIS, and coming out of it was the Doctor. He seemed to have been stumbling as he closed the door behind him. Applejack chuckled as she jumped over the fence.

“Ah never thought ah would see ya again,” she said.

The Doctor spun around. Apparently he was facing the Forest. “I come back from time to time. Sometimes not with this face,” he said.

Applejack chuckled. “Ya have been gone fer 3 years now, Doctor. That was a mighty big job ya had to do back in yer Universe.”

“I’m a time traveler, I can’t measure time outside while traveling. It could’ve been 3 years or 3 seconds. It’s good to see some things haven’t changed,” he said, looking at the barn.

Applejack spun around. “Twilight got a new library, Rainbow made it to the Wonderbolts, and ah am the owner of Sweet Apple Acres.”

The Doctor smiled. “It’s good to know I’m on track with history.”

Applejack smiled. “So ya’ll off on more adventures with yer friend?”

“No, she has something more important to do. It’s fine, really. She is needed here in Ponyville for Dinky, so I can understand that she wants to leave,” the Doctor said.

“Ah know how ya mean. Twilight is traveling again and most of us got our own lives again,” she said.

The Doctor nodded. “This won’t be the end of her travels. If I know my Equestrian history, Twilight does a lot of digging into Luna’s maps of the Universe. Of course she is going to be traveling, although, I think I have said too much.”

Applejack sighed. “Anyway, I’d best be moving on. Planets to see, ponies to save, bets to pay, all that stuff. I owe Cadence’s father a few chickens for a bet I made,” the Doctor said.

“What was the bet?”

“Doesn’t matter, unless you would want to…”

Applejack stared at him. “…want to come with me.”

The farm pony looked over at the TARDIS. “Go with yew, inside the TARDIS?”

The Doctor shrugged. “Yeah why not? It’s going to be fun.”

“All that stuff that happened all those years ago, all that was nuthin’ to ya?”

“Just a regular day for me. I don’t mind sharing that normal day with you though. What do you say: want to come with me?”

Applejack thought about it for a moment. “Ah have mah family to look for. Ah don’t have the time to leave.”

“But that’s the thing with the TARDIS. You can come with me and you can be back within a few hours. Nopony will ever know you left,” the Doctor said. “The beauty of time travel.”

Applejack looked over at the TARDIS again. She remembered what it was like in the TARDIS when they were invading Sombra’s Stronghold inside Canterlot. The rooms she entered were amazing, but she knew that there were so many more than just a few rooms. “Anywhere in time and space?”

“Anytime and place. The past, present, and future are yours to visit. We can visit your great-grandparents back when they stumbled upon the Big Macintosh apple. We can attend Twilight’s wedding, assuming she dug out of the books, we can travel with Princess Twilight’s ‘Cosmic Exploration’ program. We can have tea with Celestia and her mother, we can go anywhere and meet anypony. The only thing stopping you from seeing it all is this decision,” he said.

Applejack turned to the Doctor. She fixed her Stetson and smiled. “Ah’m in,” she said.

The Doctor smiled and led her into the TARDIS. The interior looked cleaner, like he put an effort into fixing it up a bit. The Doctor closed the door behind him and followed the cowpony into the control room. Applejack ran a hoof on the console. The last time she saw this was on their victory day. She remembered her friends running around with everything they needed to storm Canterlot. She remembered seeing the ground forces direct from Ponyville anxious to get inside the royal city.

The Doctor released the brake and looked over to Applejack. “So, where do you want to start?”

Applejack thought about it for a moment before she smiled. “Ah want to make a pit stop before we go. Ah need to get mah stuff first.”

The Doctor nodded and watched Applejack throw open the doors. She ran across the field and into her farmhouse. He watched her leave and pulled out a book from under the console. It was the book that Twilight used to discover the secret of the Elements. The book he shut on her. He turned to the bookmarked page and read to himself:

Based on my earlier investigations, I have concluded that the Elements are alive. This theory had scared Luna a little bit, but at least I didn’t divulge what else I uncovered to her and Princess Celestia. After doing some digging, I have discovered a fatal flaw in the Element’s design.

Instead of focusing mainly on good energy and magic, it has an open defense. A defense that can be penetrated by dark magic. I’ve tested my theory using dark magic. I must say, if King Sombra knew of the Elements and turned them, there wouldn’t be a kingdom under the Sun.

The Elements magnify one’s magical arsenal and uses the magic of their choice to work. If the Elements were used with dark magic, what they would do would contradict their original purpose: to provide harmony and life. If they are turned, then they can wipe out all life in Equestria. If this comes to be, the Elements of Harmony will be no more.

They will bring Armageddon. They will become the Elements of Disaster.

-Starswirl the Bearded

Applejack returned with a box strapped onto her back. The Doctor immediately hid the book under the console. With a destination from his companion, the TARDIS doors slammed shut and immediately dematerialized.

Trixie fidgeted in her nightmare. The two years she spent traveling across Equestria bore little fruit. Her wagon was paid off thanks to a grateful soul in Ponyville, her magic began expanding, and more ponies started noticing her. She could say it was amazing, but she always appeared AFTER princess Twilight. Twilight was the main event and Trixie was the shadow that followed. It didn’t help with her magical hat being damaged in the war a few years back.

Ever since the changelings ruined her hat, she had a violent reaction every time one appeared before her. Each time she fought and beaten a changeling, she remembered the little voice in the back of her head screaming ‘A wizard is nothing without a hat!’ Trixie had parked her wagon on a tree at the top of a hill. She was to perform at Trottingham in the next few days, and she was a month ahead of Twilight. She sighed in her empty wagon.

Suddenly, there came a knock on the door. Trixie heard it but didn’t move. Probably a prankster leaving a bag of unmentionables again, she thought to herself.

Another knock broke the silence. Trixie groaned as her dream ended and she was pulled back into reality. She looked up at the door.

Another knock came in, and Trixie sighed. “Who dares disturb the Great and Powerful Trixie?!”

She heard a thud on the ground. There was one more knock, and the sound of a pony running away. Trixie sighed as she pulled out a brick from under her bed. She grabbed the door knob with her magic, and threw it open. She raised the brick to find that nopony was there. The night was still around and crickets chirped in the night. The only difference in that scene was a brown box sitting at her doorstep. She looked around, looking for the mailmare who delivered it. On the box was a note.

Trixie picked up the note. It read A wizard is not without her hat.

‘Oh great, my nightmare is real,’ she thought. She opened the box and caught her squeak.

Inside was her hat fully patched up. She grabbed the hat with her magic and placed it on top of her head. Suddenly, she felt something sharp poking at her head. She raised the hat, and a metal rod fell out. It was a magic wand with another note on it.

‘Thank ya fer helpin’ with Ponyville all them years ago. Try and not get ponies upset.
-AJ’

She smiled as she raised the wand. She looked around and still saw nothing. The only things on the hill was a tree, and…a blue box? The brightly lit box stood there, staring at her. She did not know why, but Trixie found herself waving at the box. She picked up the box and wand, and reentered her wagon. The last sound she heard before falling back to sleep was the sound of the engines of the TARDIS fading into the dark.

Epilogue: New Enemies Rise!

Tartarus.

Do you know where the monsters go once they’re defeated? Do you know what happens to the worst souls in Creation? The souls not even Hell would accept fall into Tartarus. In Tartarus, you would wish for Hell. At least you would be given a break from time to time.

The dark cavern that concealed the worst creatures had always been a place to experience pure fear and torture. Ponies, humans, aliens, gods and so many more evil creatures were sent to Tartarus for a minimum of at least 5 life sentences. To the worlds beyond, Tartarus was where villains were reformed. For some, it was the perfect place to carry out hatred on souls who deserved it. For others, it was a fate worse than death.

For the very few, it was home.

The wastelands of Inner Tartarus was suddenly greeted by a gray blur speeding through the valley. The blur raced past some geysers currently occupied by damned souls from other dimensions. The very souls tried to cry out to the blur for help, but their cries bore little fruit.

The blur raced throughout the prison. The further it went, the worse the monsters and the tortures were. The blur jumped over a bottomless pit and toward what appeared to be a stone castle. The castle took up the very end of the endless chasm. Built out of red stone with dragons guarding the entranceway, the castle held a giant sign that said KEEP OUT!

No, seriously. Right above the castle is a neon sign that says KEEP OUT!

Ignoring the obvious signs of danger, the blur raced through the obsidian gates and past the dragon guardians. Unlike Equestrian dragons, these dragons were all violet shaded with piercing red eyes. Each dragon had three heads, two of which were on lookout while the third was asleep. The dragons saw the blur race past them but thought nothing of it. Soon, the other heads were fast asleep.

The blur blasted through the doors and up staircase after staircase, winding around towers and flying through floorless corridors.

The blur stopped in front of large black doors. In its still place was a creature of human appearance. The creature was wearing a black leather coat with obvious holes in the shoulders and back area. He wore a black T-shirt with a skull pendant necklace around his neck. He also was wearing gray cargo packs with army boots to match. His head was covered with a plastic skull mask with a large golden crown hanging off the side of his head.

The creature kicked open the doors to the room and spread his arms out wide. “GUESS WHO’S BACK?!” he announced.

The room his was in was basically empty aside from the hooded man kneeling in front of a throne and a woman in black armor pacing the open space in front. The woman cursed upon laying her red eyes on the skull-masked individual. “You’re late again Kraos,” she said.

The figure, Kraos only laughed. “If anyone is late, it’s our bastard brother who has yet to show his face around here! 20 millennia and all we get is a summons? If I wanted to be humiliated by a summons, I would go to jury duty.”

The hooded figure laughed as he rose from in front of the throne. “You? The Mad King Kraos sitting down in a jury? If that were to happen, I would give my godhood to a mortal!”

The two men laughed as the woman sighed as she continued to pace the room. “You both are idiots, you know that?”

The Mad King wiped a tear from his mask. “Oh please, you find us hilarious and you know it! God of Madness? Hell, make me the patron god of Court Jesters!”

“Now there’s an idea.”

The three individuals froze as the new voice echoed throughout the room. The hooded figure raised his head as the throne was consumed with black smoke. In a second, the smoke turned red as a new figure appeared. Like all the others, this figure was human in appearance. He wore a blood red suit and tie with black slicked hair. His eyes shone with the power of the Universe.

On instinct, the three other individuals bowed before the man at the throne. The woman was the first to speak. “M-my Lord.”

The man raised his hand at the woman. “Please, no need for formalities yet. I am simply curious about the state of the operation. Kraos, was it successful?”

The Mad King shook his head. “They have been defeated, my Lord. It has just been recently as well.”

The red-suited man growled. “And your research has proven—?”

“Positive. The Elements of Harmony can crack.”

The man smiled, bearing a single canine tooth. “Excellent, now we move onto step two. You all have what you need to do?”

“Yes my Lord!” the three said in unison.

The man turned to the hooded figure. “Hypnos, I want you to return to the other dimension and see what you can do in generating enough energy to break the seal on my castle.”

“Thy will be done, my Lord,” the hooded figure said.

“Darklight, I want the royal family eliminated immediately. If we are to get our hands on the Elements, we need to ensure we will not be disturbed by them at all. I don’t care how, just do it. Bring the Elements intact,” the man ordered.

The woman grinned. “Thy will be done, my Lord.”

“Kraos, I want you to tail the Time Lord. Do not make yourself known until I say to. If the information is correct, then we should have no problem in gathering the information we seek.”

“Got it boss,” the Mad King said.

The red-suited man growled. “You’re all dismissed…”

The three turned to walk out. “Except you, Kraos.”

The Mad King froze. The hooded figure, Hypnos chuckled. “Good luck.” Hypnos turned to smoke.

Kraos sighed and spun around, readjusting his crown in the process. “What’s up?”

The red-suited man said nothing. He approached the Mad King and backhanded him through a series of columns before landing on the stone balcony just outside the room. Kraos rolled to a stop and groaned in pain.

The red-suited man simply walked over to the Mad King and sighed. “I gave you a chance to redeem yourself, but once again, you failed!”

Kraos slowly rose up. “Six little ponies banded together and defeated your little regime change like it was nothing. That is embarrassing Kraos!”

“M-my Lord, even they caught me by surprise! I was certain…”

“Taking over the mind of the god of Chaos was not the way to go. I asked you to find me any information regarding the Elements of Harmony, but you failed me! Give me one good reason why I shouldn’t banish you to the lower rings of Hades!”

Kraos said nothing. He reached into his coat and tossed a blue box at the red-suited man. He caught it swiftly and closely inspected it. “What is this?”

The Mad King smiled. “The Harmony Prophecy. A prophecy that foretells the end of Equestria by the hooves of the leader of the kingdom of twilight. I found her, my Lord. I found Twilight Sparkle.”

The red-suited man flashed a wicked grin. “Consider yourself lucky, Kraos. Don’t make me have to repeat this conversation.”

The Mad King bowed. “Thy will be done, my Lord.”

The red-suited man walked away with the Chest in his hand. “Twilight Sparkle: the Princess of Friendship and the Destroyer of Equestria.”

Kraos laughed maniacally. “This will be fun.” The red-suited man vanished in a cloud of red smoke, leaving the Mad King alone in the throne room.

Author's Note

This is the end of Dark Vengeance at last. Thank you to the people who actually liked this story. Yes, I will continue with Whooves N' Jack in a little bit.

Flutter On!