Equestria Ninjas: Shadow Play

by Wildcard25

Rating: everyone
Tags: Starswirl the Bearded, Starlight Glimmer, Teenage Mutant Ninja Turtles, Sunburst, Crossover, Tragedy, Main 6, My Little Pony: Friendship is Magic, Other, Drama, Mystery
Length: 15708

The Ninjas of New York and Ponies of Equestria band together to rescue the legendary heroes of Equestria and defeat the enemy they fought a Thousand Years ago.

The turtles and their human friends return to Equestria to uncover the truth behind the disappearance of Star Swirl the Bearded and the Pillars of Equestria. But will discovering the truth lead them to an even bigger problem?

This fic contains no spoilers from Equestria Ninja Girls Rainboom and Crystal Ninjas

Published 2017-11-12 03:50:06 UTC
Last updated 2017-11-13 01:09:01 UTC

The Pillars of Equestria

Author's Note

Don't be alarmed. I know I had also just started another fic like this featuring the Equestria Girls going back to New York with their school and Crystal Prep. But I assure you this fic contains no spoilers from that one.

The Pillars of Equestria

In the turtles lair, Leo and Karai were sparing in the dojo, Mikey was showing Shini one of his comics, April, Donnie, Raph, and Casey were watching another episode of Space Heroes the Next Generation. Raph spoke, "Man, It's been over a week since we had any action."

"I hear ya," Casey agreed, "There hasn't been any crime activity as of late."

"Well, maybe it's good we're finally getting a break." April noted.

"Yeah, but too big of a break can get boring after awhile." Mikey replied.

Leo came in with Karai and spoke, "Which is why we must also be prepared for when and if the time comes when we need to be at the peak of our strength."

"Well, something better happen soon, or I'm gonna go crazy." Raph said in irritation.

"And I thought you did years ago." Donnie replied.

"Ha! Good one." Mikey laughed.

Raph was ready to jump Donnie, until they saw sparks cracking out of thin air, and suddenly a portal appeared, "Uh, Donnie, what is this?" Casey asked.

"I don't know, all I do know is it's a gateway." Donnie answered.

"But to where?" Shini wondered.

"Guys!" came a familiar female voice from the other side of the gateway.

They saw it was Princess Twilight Sparkle and Starlight Glimmer using their combined magic prowess to open the gateway, "Twilight?" Leo gasped.

"Starlight?" Karai asked.

"Guys, you have to come through the portal. There's something you have to see." Twilight instructed.

The ninjas looked at each other, as April spoke, "Well, we have been wanting something to do."

"Then let's go." Leo ordered, as the group grabbed their gear and went through the portal as it closed.

On the other side of the portal in Twilight's castle, the turtles and their human friends appeared in their anthro or normal pony forms, "We made it." Mikey cheered, as he and his bros checked their anthro pony forms out.

"And in one piece." Donnie added.

"You know no matter how many times you go through a portal to another dimension and taking on another form, you never quite get used to it." Karai told Shini, Casey, and April.

"It's good to see you guys again." Twilight smiled.

"And it's great to see you too, Twilight." Leo smiled back.

"How did you manage to open a portal like that without using the one located at CHS?" Donnie wondered.

Starlight spoke up, "Well, Twilight and myself pondered on it and using our combined magic prowess and magic from the mirror portal, we were able to create our own portal spell to any part of your world so long as we've been there already."

"And we were able to open a portal right to the lair," Twilight concluded, "We're just lucky you were all there."

"Not much action going down in the city, unfortunately." Casey sighed.

"So what's the big call?" Raph inquired.

Starlight began, "Well it all started when Sunburst came for a visit, which is good because he is my oldest friend after all. But then he started finding out he had a lot in common with my other friends, so I desperately tried to find another way to bond with him, but I ended up turning us back into foals..." April spoke up.

"Maybe you should cut to the chase?" she suggested.

"Oh, right," Starlight grinned sheepishly, "After Sunburst left, we suddenly got a message from Princess Celestia to come to Canterlot asap, because Sunburst found something very important."

"Did he say what?" Leo inquired.

"Only that it's something that may change everything we know about Equestria history," Twilight answered, "And I wanted you guys here in case it was going to be something really big. Because let's face it, things tend to get big when something comes up."

"No denying that." Raph replied.

"So come on, we better get going." Twilight instructed, as the group headed for the train station to rendezvous with the others.

After a train ride to Canterlot, the crew made their way to the castle, and who should be waiting for them but Blade Swipe wearing guard armor and a helmet, "Blade!" the ninjas greeted.

Blade smiled, "Hello, old friends. It's good to see you all again."

"Feeling's mutual." Leo agreed.

"Based on the armor, I say you're doing very well." Karai noted.

"Yes. Being a guard in Canterlot has always been my dream, and now I'm finally living it."

"Well then, Blade Swipe, be a dear guard and take us to the Princesses." Rarity instructed.

"As you wish." Blade bowed his head before escorting them inside.

As they reached the throne room, they saw waiting for them was the Royal Sisters and Sunburst. Blade announced, "Presenting, Princess Twilight Sparkle and Company. And also presenting, the Ninjas of the other realm."

Starlight trotted over to Sunburst, "Good to see you again, Sunburst, even if it hasn't been that long."

"I know." Sunburst chuckled.

Celestia spoke to the ninjas, "It's good to see you all could come. How have things been in your world?"

"As of late, dull." Leo admitted.

"Well, you won't find it dull after you hear what I found." Sunburst replied.

"What did you find?" Twilight asked.

Sunburst levitated a an old musty book up, "I found this journal among the other contents from the mystery barrel I bought during my visit."

"What's it about?" Applejack asked.

"Prepare yourselves." Sunburst began as he opened the journal and started reading it's contents. As he read an older male voice narrated.

The best elements within us can spread light and virtue, and I know ponies who represent them all – strength, bravery, healing, beauty, hope, and sorcery. Myself and these Pillars of Equestria were gathered together by another to maintain and share the light of these powerful ideals. But we soon came to believe the pony who brought us together only wanted that power for himself. Cast out and alone, this power-mad pony turned to darkness to satisfy his thirst. Transformed into a Pony of Shadows, he returned for revenge – to extinguish the Pillars' light and rob the world of hope. To stop him, the Pillars and I must make a grave sacrifice. But we shall leave behind a seed in hopes that one day it will grow into a force to stand against the darkness for all time. We must now face the fiend with the only plan we have...

It concluded with Sunburst reading the final line, "I only hope it will be enough." That's the last entry. And maybe Star Swirl's final words before he vanished." the ponies were shocked, while the ninjas were confused.

Princess Celestia levitated the book over to her and Luna so they could inspect it. The Princess of the Sun spoke, "I've always wondered what happened to Star Swirl. This is quite a discovery, Sunburst." she commended him.

Sunburst did a bow, as Twilight asked in shock, "So it's genuine? You can verify that this journal really belonged to Star Swirl the Bearded?!"

Luna nodded, "Indeed. From the looks of it, the last thing he wrote before facing the Pony of Shadows."

"Uh... So, the Pony of Shadows was really real?" Rainbow Dash asked sounding a bit nervous.

"It appears so." Celestia confirmed.

"We never met the other Pillars, and we were too young to understand the danger they faced." Luna explained.

"Hold on a second now," Applejack spoke up, "All those legendary ponies were real, too? And they went off with Star Swirl to face the Pony of Shadows, and then none of them were ever heard from again?"

Pinkie spoke up while nudging A.J, "Uh, yeah. Weren't you listening?" she grinned

"But what happened to them?" Fluttershy wondered.

Rarity answered, "They must have defeated the villain, since Equestria is still full of light and hope."

"But how? And where did they go?" Starlight asked.

Celestia looked at the journal contents, "My Olde Ponish is a bit rusty, but I wonder if the answers can be found somewhere within the pages of this book."

Twilight began boasting, "Well, I just happen to be an expert in Olde Ponish. I mean, I've practically memorized every ancient text about Star Swirl there is!"

Spike face palmed himself, "Seriously. All of them." he confirmed dryly.

Luna spoke, "We have fond memories of our old teacher. If you could discover what happened to him, we would be most grateful." she levitated the book to Twilight who grabbed it, while looking excited.

"Solving a thousands-year-old mystery could take forever! Think of the research! The re-reading! The re-re-reading!" Sunburst said giddily, while holding his hoofs to Spike and Mikey who fist bumped with him, but didn't look as thrilled.

"You might find you need help." Celestia noted.

Applejack spoke up, while motioning to Twilight, "Luckily, she's got a whole bushel o' helpers right here." Everyone stood behind her.

"Totally!" Rainbow agreed, "Uh... how long will all this research take, exactly?"

"Let's get this back to my library. I'm sure we'll figure out what happened in no time." Twilight said, as they were about to leave, until Raph called out.

"Hold it!" everyone turned to Raph, feeling startled by his outburst.

"Whatever is the matter, Raphael?" Rarity asked in concern.

"Is anyone here going to explain to us what's going on?" He asked.

"Yeah. Who is this Star Swirl?" Shini asked.

"And what're these pillars?" Leo wondered.

Twilight spoke up, "Well, Star Swirl the Bearded was regarded as one of the most powerful unicorns in Equestria. His knowledge of magic was unrivaled by any. The creator of more than 200 hundred spells. One of which I finished for him, thus granting my princess title." she blushed.

"And he was the one who banished the Dazzlings from Equestria to our world?" Karai asked.

"Exactly." Twilight confirmed.

"So who are the pillars of Equestria?" Donnie asked.

"Originally they were believed to be legends and bedtime stories, but apparently they were real." Blade explained.

"I'll tell ya'll about the one that's my personal favorite, the Legend of Rockhoof." Applejack began telling the tale.

Rockhoof was known far and wide for his incredible strength. But he didn't start out that way. You see, Rockhoof was a tiny little fella, the son of a farmer. They lived in a village that sat at the foot of a gigantic volcano. And the village was protected by an elite group of guard ponies called the Mighty Helm. Young Rockhoof wanted nothing more than to be part of the Mighty Helm. But he was told that he was too scrawny and weak to protect the village.

"Wow the Mighty Helm sounds kinda mean." Mikey said, only to get shushed by his brothers. Applejack continued.

But Rockhoof wouldn't take no for an answer. Then, one fateful day... the volcano erupted! The molten lava poured down the side of the volcano... and try as they might, the Mighty Helm couldn't figure out a way to save the village! They had to evacuate. But the village ponies didn't wanna leave their homes. They spent their entire lives there. They had nowhere else to go! So Rockhoof decided to do something crazy. He thought if he could divert the flow of the lava, he might be able to save his village. He started diggin' a trench!

"By himself?" April asked.

"Digging a trench fast enough to stop lava by yourself is impossible." Donnie stated.

"Good thing Rockhoof didn't believe in the word 'impossible'." Applejack smirked, and continued narrating.

He continued to work, knowin' the odds were against him, but determined to push through it. Then, somethin' magical happened. Rockhoof got visibly stronger! But the lava was getting' closer. Through his extraordinary determination and sheer force o' will, Rockhoof more than earned his place in the Mighty Helm.

"Whoa," Casey gasped, "Rockhoof sounded like an awesome dude."

"Especially what he was trying to do to save his fellow ponies." Leo added.

"Just one of the reasons I was always fond of his story." Applejack smiled.

"So who're the other ones?" Mikey asked.

Rarity cleared her throat, "Allow me to tell you a tale of a pony named Mistmane, a pony who saw the beauty in everything." she offered, and began narrating.

Mistmane was once the most beautiful unicorn in all the land, and a very promising young sorceress. She was as talented as she was beautiful and kind. Everypony loved her and missed her when she was sent to the finest magic school. While she was gone, she was delighted to find out that her best friend, Sable Spirit, was crowned empress. She couldn't wait to return home once she finished her studies. But once she arrived, she was devastated by what she saw.

"What happened?" Mikey asked nervously.

Empress Sable Spirit made everypony work day and night on her palace. Leaving them no time to take care of anything else, including their own homes. Mistmane refused to believe the accusation knowing her friend too well, but there was no denying what was in front of her. Sable Spirit took everything that was beautiful away from anypony else! And Mistmane was sure there had to be some explanation.

"Sounds like Sable Spirit was a real Vanity Queen." April noted. Rarity continued to narrate.

Mistmane went to confront her friend to discover Sable Spirit was old and horrid. She wanted her palace to be a beacon of beauty and everypony would be awed by its majesty. Sable Spirit told Mistmane that it was she who taught her beauty was everything. She was jealous of Mistmane always being praised so she attempted to perform a spell that would make her equally beautiful, but it went horribly wrong. She declared if she couldn't have beauty then she would take it, just as she took the title of Empress instead of being given it.

"Yeah that's a vanity queen for you." Raph confirmed.

Mistmane fought Sable and defeated her. Everypony thought Sable Spirit was defeated, and that was that. But Mistmane knew there was more she could do to help. Beauty isn't everything. But Mistmane knew that it does have the power to make ponies smile. She made a huge sacrifice to bring that smile back to her friends' and family's faces... including Sable Spirit's. So she gave up her own beauty to everypony including Sable's. Sable Spirit was so touched that she vowed to be more like her friend in the ways that mattered. From then on, she ruled with kindness and compassion. Even though she gave away her physical beauty, she dedicated her life to spreading beauty all over Equestria. Any time you go out of your way to brighten somepony's day by doing something like giving them flowers, you're following in the hoofsteps of Mistmane.

"Wow, that's beautiful." Shini gasped.

"And touching." Mikey shed a tear.

"Yeah-yeah, but you guys wanna hear a real legend?" Rainbow asked getting them pumped.

"Sure. What've you got?" Leo asked.

"This is the story of one of the best ponies next to me, Flash Magnus." Rainbow began narrating.

A long time ago, before the Wonderbolts were even founded... Flash Magnus was a lowly cadet in the Royal Legion. And the Legion needed to fly over the Dragon Lands to get to their comrades on the other side. But as they got closer to the dragons... the dragons attacked!

Mikey got scared and clung to Donnie who pried him off. Rainbow Dash continued with the legend.

Flash Magnus and the Royal Legion tried to get past the dragons... but the dragons wouldn't let them. Flash Magnus and a few other cadets were separated from the battalion. He managed to get away, but the dragons captured his friends and took them back to their lair! Flash wanted to rescue his comrades, but the commander felt there was no way to get past the dragons. Flash offered to be a decoy to lure the dragons away so his comrades could save the others. The commander gave Flash Magnus Netitus, the fireproof shield to help him. The shield has protected Legion heroes for generations, and he had deemed Flash worthy to use it. While Flash Magnus bravely flew for his life, Commander Ironhoof was able to get his soldiers back. Flash flew like the wind faster than the dragons. But Flash knew he couldn't do this forever. Luckily, he had a plan.

"What did he do?" Raph wondered.

He led the dragons straight into a storm that the Legion had planted! One taste of the lightning, and the dragons retreated. Flash Magnus' plan worked, and their comrades were saved.

"Now that's true bravery." Leo admitted.

"I know, right?" Rainbow asked.

"And what of the other ones?" Karai asked.

"Ooh! Ooh! Me next! Me next!" Pinkie cheered, "This story is about a pony named Somnambula who had a village named after her." she began narrating.

A long time ago a village fell prey to an evil Sphinx who demanded most of their crops. Like her fellow villagers, Somnambula didn't have much, but she used what she had to keep others from giving up hope. The son of the Pharaoh, Prince Hisan, was so moved by her compassion that he decreed nopony would go hungry again. But when Hisan stood up to the Sphinx, the beast captured him, telling the Pharaoh the only way to get Hisan back was to solve her riddle. Nopony would volunteer to save the prince. Nopony except Somnambula. The Sphinx gave her the riddle. "I shine brightest in the dark. I am there but cannot be seen. To have me costs you nothing. To be without me costs you everything." As Somnambula thought of the hardship she and her fellow villagers had experienced, she instantly knew the answer. "Hope!", she shouted.

"That was easy." Donnie admitted, as Pinkie continued.

The Sphinx was so enraged, it seemed she might still refuse to release the prince, so Somnambula asked her for one more challenge. But if she accomplished it, the Sphinx would leave from the kingdom forever. The Sphinx quickly agreed, asking only that Somnambula walk to the prince across a deep chasm... blindfolded! Further, the Sphinx had cast a powerful spell that prevented Somnambula from flying. But Somnambula never lost hope! She knew she'd need to make a leap of faith to save the prince. Guided by the sound of the prince's voice... she easily made it across. The Pharaoh asked how Somnambula prevailed, and she explained that she had always hoped she could make things better for her people and that hope had carried her through. The Prince replaced the pearls Somnambula gave up with a string of glowpaz. And around her neck, they glowed bright enough to light the entire kingdom.

"Amazing to hear how much hope she had in herself." Karai admired.

"Sometimes having hope is all you need to tip the scale in battle." Leo noted.

"And the last pillar, who is it?" Donnie asked.

"Um, if it's ok, could I tell this one?" Fluttershy asked, as the princesses confirmed, "Ok, this is the story of Mage Meadowbrook, a pony best known for making healing medicines." she started narrating.

Long ago, she studied medicine under her mother and kept multiple journals. In one of her journal entries, Meadowbrook discussed how she dealt with a Swamp Fever epidemic that infected her mother and fellow villagers. While searching for a cure, she discovered that flash bees are immune to the disease-spreading flower's poison. Using her healer's mask to shield herself from the bees, Meadowbrook collected some of their honey and used it to develop a cure for the epidemic. Afterward, she dedicated her life to helping other sick ponies across Equestria.

The ninjas were astounded by the stories they were told, as Leo spoke, "So like Starswirl, those legendary ponies vanished with him?"

"Exactly." Sunburst confirmed.

"And who is this Pony of Shadows?" Casey wondered.

Blade spoke up, "Legends had it that many years ago when Nightmare Moon was banished to the moon, traces of her dark magic stayed behind in the walls of the Castle of the Two Sisters," he motioned to the Royal siblings who nodded, "When night falls onto their castle, that dark magic takes the form of the Pony of Shadows. But based off this new information there's more than what we were led to believe."

Celestia nodded, "Now that you know of our legendary figures, I trust you will help our subjects in uncovering the truth to what happened to our mentor and the others?"

Leo stepped forward and answered, "You can count on us, Princess. Ninjas, let's go uncover this mystery together."

"Oh, yeah boy!" Mikey cheered.

"Well, we got nothing better to do." Casey admitted.

"As long as most of the studying is handled by the eggheads." Raph motioned to Donnie, Twilight, and Sunburst who scowled at his insult.

"Come on let's go." Twilight said, as they all hurried back to Ponyville.

Celestia turned to Blade Swipe and spoke, "Go with them, Blade."

"Princess?" he asked in surprise.

"They will need as much help as they can get. And I have a feeling things may take a surprising turn. So I want you to join them and protect them." she instructed.

Blade bowed his head, "I shall protect them with my life, Princess Celestia. On my honor as a Royal Guard and ninja, I shall not fail." he went after the others.

Locate the Artifacts

After discovering that Star Swirl the Bearded and the Pillars of Equestria had vanished, the girls and their friends from New York set out to uncover the source behind their disappearance. They were confident enough they could crack the case with no problem.

Three days later at Twilight's castle library, Twilight and Donnie were at a table surrounded by books and scrolls. Everyone else was practically fast asleep from reaching their limits with reading. Donnie and Twilight felt they could find out what happened to the pillars, but from the looks of things they kept reaching a dead end. Spike came in holding a candlestick, "Find anything yet?" he asked the two. Twilight just shook her head, as Donnie spoke.

"And I thought trying to make retro mutagen was tough, but this is ridiculous." Donnie said, as he tossed a scrunched up piece of paper into a wastebasket.

This caused Sunburst who was lying underneath a pile of scrolls to rise up, "What did you figure out?"

Pinkie yawned, as she and the others started waking up, "You figured something out?"

"What is it?" Fluttershy inquired.

Twilight sighed and shook her head, "Nothing. I mean, Star Swirl was a genius, obviously. But forget Olde Ponish. There's parts where his hornwriting is like another language!" she groaned.

"Twilight, we've been studyin' and referencin' and cross-referencin' for three days straight now." Applejack noted.

"Yeah. Even I've never done that this long." Casey admitted.

"Since when did you ever study at all?" April asked rhetorically.

"Ouch." Casey cringed.

"Ugh. I haven't spent this much time reading since the last Daring Do book came out." Rainbow Dash groaned.

"Same with me and my latest comic issue of Wingnut and Screwloose." Mikey added.

"Perhaps it is time to take a break," Rarity suggested, "This mystery is over a thousand years old, after all. Another day or two won't make a difference."

"I agree with Rarity." Karai agreed.

"Two days?!" Twilight gasped, "I don't wanna waste two seconds!" she trotted over to a graph on a chalkboard, "I'm close to an answer. I can feel it."

"Well, until you reach one, I need something in my belly." Raph said.

"Yeah, we could all use a bite." Leo agreed.

Starlight trotted over with tea before checking a passage in the book, "Hearg sylfum se Ponhenge. What's that?"

Twilight slid in and gasped, "The Temple of Ponhenge?! You can read that?!"

"The hornwriting's pretty sloppy, but it's nowhere near as bad as mine." Starlight admitted.

"Well, go on and read it." Shini beckoned her.

Starlight nodded, and continued, "Toward dol grimlic of Fola Firgenbeorg?"

Sunburst spoke as he translated it, "At the base of Foal Mountain."

"User endemest scield." Starlight read.

"Our last stand!" Twilight gasped.

Spike yawned, "Well, that sure sounds like a clue to me." he got comfy on a big pillow and fell asleep.

Mikey turned to his brothers, "And you all call me lazy."

Donnie placed a book down on the table to show them a map of the place they were talking about, "Is that the place?" he asked.

"It is," Twilight confirmed, "And that's where we need to go."

"Then let's get going." Leo stated, as the group took the book and left the castle.

Soon they arrived at the Foal Mountain and saw some rock formations like pillars, "This is it. Ponhenge. I can't believe it." Twilight gasped.

"This place looks like it's seen better days." Blade noticed all the heavy bushes and vines surrounding the place.

"It's just like Stonehenge in our world." Donnie gasped.

Sunburst saw writing on one of the rocks, "I've never seen magical runes like these before! Have you?"

"Uh-uh." Twilight replied.

"I don't think anypony's seen any of this for a long time." Rainbow noted, as she tried to pull a vine off one of the rocks only to crash into a bush.

"It'd take a whole team of ponies to clear away all this brush." Applejack said.

"Well, we're a team of ponies, aren't we?" Casey asked.

"Even then, I'm not sure we'd find out what happened here over a thousand years ago." Fluttershy added.

Twilight sighed, "You're right. I suppose it was a long shot."

Leo spoke to her, "Twilight. Finding a whole set of ancient ruins is pretty impressive alone. You could write a paper on it."

"It's better than nothing." April agreed.

"I guess I hoped we'd get here and the mystery would just magically be explained." Twilight said, as she dropped Star Swirls' book at one of the rocks. Suddenly the book started glowing, and Spike spoke.

"Uh, Twilight." every pony looked and saw the book flipped open and released a magical aura.

"What's going on?" Shini asked.

"I don't know." Raph replied.

Suddenly appearing above the book was an astral form of Star Swirl the Bearded, "Whoa, is that?" Leo began.

Twilight gasped, "Star Swirl!? I... I've wanted to meet you my whole life! I can't believe you're here!"

"He doesn't look all here." Mikey said, noticing his transparency.

"I don't think any of them are." Sunburst added.

The group saw appearing at the other rock formations were five more ponies, "No way." Casey gasped.

"Are they really?" Donnie asked.

"The pillars." Sunburst gasped.

"What is this?" Karai asked, only for Star Swirl to shoot magic at the centerpiece of the rock formation and appearing before them was a big black clouded figure of an evil alicorn.

"You summon me at your peril, Star Swirl!" the creature asked, "Once I defeat all of you, this realm will embrace the darkness as I did so long ago!" Mikey began screaming his head off in a panic, as the other watched in shock.

"I'm going out on a limb here and guess that's the Pony of Shadows?" Casey shook in fright.

The Pony of Shadows ensnared the six legendary ponies with black shadowy vines to hold them at bay, "Drawing me here will only make me stronger. You will never defeat me!" he laughed evilly.

"We did not come here to defeat you." Star Swirl began as he levitated his book up which sent a magical link to various other artifacts held by the other pillars forming a hexagon shape around their enemy.

"What are you doing?" the Pony of Shadows asked in shock.

Star Swirl answered, "We came... to contain you."

The dark pony screamed as the seven of them levitated up and vanished into thin air. Dropping at each of the stones was an artifact each, a shovel, a flower, a shield, a mask, a blindfold, and a book. Everyone was still in shock from what they witnessed, except for Pinkie Pie who spoke to Twilight, "Well, you did ask for a magical explanation."

"What just happened here?" Raph asked then group.

"It looked like Star Swirl cast a spell that banished the Pony of Shadows." Starlight answered.

"Of course!" Sunburst gasped, "Powerful magic like that would leave an impression on this place. Bringing the book back here let us see what happened."

"Which was what?" A.J wondered.

"Star Swirl and the rest of the Pillars sacrificed themselves to save Equestria." Twilight stated.

"Wow, that is a big sacrifice." Mikey gasped, as they all agreed.

The next day back at Twilight's castle, the group was still pondering over what they saw last night at Ponhenge, "It's amazing to think one of the greatest mysteries of Equestria was solved with a musty old book from an antique shop." Starlight said.

"But I wouldn't say the mystery's solved. Star Swirl's spell was one of the most powerful feats of magic in all of history. It'll take years of study before we fully understand it." Sunburst noted.

"I ain't doing anymore studying." Raph replied, as they entered the library to see Twilight pop out of a pile of books looking excited "I think I understand Star Swirl's spell!" she declared.

"That was quick." Karai said.

Soon enough everyone was in the castle throne room, with the girls at their respective thrones. Twilight began explaining to everyone, "I know I've finished one of Star Swirl's spells before, but this one was on a whole different level! Was it an explosion of magical feedback? An evocation? A kind of incantation? It's Star Swirl, so the possibilities are endless! And once Starlight set me on the right track with his crazy hornwriting..." she laughed and snorted, "I mean, he was a genius, so I guess we can forgive a little messiness – I went through the journal again, and it's amazing!"

"Get on with it!" Raph and Casey snapped.

Rarity spoke calmly, "Twilight, darling. We understand you're excited, but that's all we understand."

"What exactly is so amazing?" Shini asked.

"Don't leave us hanging, girl." Mikey added.

Twilight continued, "Only how Star Swirl and the other Pillars sent the Pony of Shadows to limbo!"

"They did what now?" Applejack asked.

"Where'd they go?" Blade inquired.

Twilight levitated a diagram of Ponhenge onto the table, and concentrated magic in the center of it, "They used their magic to open a portal between worlds – to limbo – and pulled the Pony of Shadows inside." the diagram poofed away.

"Darling, your diorama!" Rarity gasped.

"It was so nicely done." Mikey whined.

"I made more!" Twilight cheered, as she motioned to many more Ponhenge dioramas on another table, "Star Swirl thought the only way to trap the Pony of Shadows in limbo was for the Pillars to take him there."

"So they got stuck too?" Applejack asked.

"Bummer, yo." Casey said.

"The Pony of Shadows must have been really awful for them to do that." Fluttershy shivered.

"I suppose being trapped for all time with a super-duper bad guy in limbo might be okay if you were doing the limbo, but that's still pushing it." Pinkie said, as she was literally doing the limbo.

"The thing is, I think I can get them out." Twilight stated with confidence.

"You can?" Leo asked.

Sunburst spoke, "Twilight, are you serious? You can save the most legendary ponies of all time?"

Starlight voiced her opinion, "I-I don't know. Opening portals between worlds didn't work out well for me. Are you sure it's safe?"

"Yeah, the last thing we need is something worse to happen." Raph added.

Twilight spoke to Starlight, "First of all, you opened portals through time. And second of all, Star Swirl wrote the spell you used to do it. If he'd been here, he could have stopped it. Equestria would be safer with him in it. We have to save him."

"And the others." Mikey added.

"But you'd be savin' all the Pillars, right? A-And they disappeared ages ago." Applejack reminded her.

"That's the thing about limbo. It isn't one place or another. It's in between, so time stands still. If we can pull them out, it'll be like they never left," Twilight explained, "I actually built another model to demonstrate..." Rainbow groaned and slammed her head onto the table.

"I don't think we'll need to see another model. We'll take your word for it." April told the Princess.

"What can we do to help?" Blade inquired.

"If I'm right, we need to find items that are connected to the Pillars in some way." Twilight answered.

"You mean, like, stuff that belonged to them?" Donnie asked.

"But that'll take too much time." Raph reminded her.

"We don't know what to look for or where." Fluttershy added.

"Luckily, Star Swirl took a lot of notes," Twilight read the notes, 'My compatriots are as varied as the realm itself and hail from every corner of our land, bringing with them artifacts and talismans of great power'."

Suddenly appearing before them were shining images of certain artifacts, "Twi, what're you doing?" Leo asked.

"I'm not doing anything!" she gasped.

The five artifacts went to a different spot on the cutie map, as the girls identified the objects, "Rockhoof's shovel!" A.J gasped.

"Flash Magnus' shield!" Rainbow Dash identified it.

"Mistmane's flower!" Rarity noticed.

"Meadowbrook's mask!" Fluttershy gasped.

"And the blindfold Somnambula wore when she faced that nasty sphinx!" Pinkie finished.

"I guess we don't need to figure out who should get what." Twilight said.

"Yeah, we know what they are and where they are now." Donnie added.

"All right, team. New mission," Leo began, "We find these artifacts and bring them back to Ponhenge."

Somewhere by an archaeological dig sight, a filly named Petunia Paleo motioned to something that was uncovered, "Professor! It's a Mighty Helm headpiece! Maybe it belonged to Rockhoof himself!"

The Professor answered, "Legends don't wear helmets. This belonged to a real pony."

Applejack came over with Casey, "Oh, I can guarantee Rockhoof was as real as you and me." A.J assured them.

The Professor chuckled, "And I suppose that ravine was dug with his trusty shovel to save the village from an erupting volcano."

"You bet it was." Casey confirmed.

"I love old legends as much as anypony. But a pony strong enough to save a village from rushing lava with a shovel is... preposterous." the professor said skeptically.

One of the ponies who was picking at a boulder with a pickaxe shattered it, putting the other ponies in shock causing a giant boulder to roll right for the professor and the two kids she was with. Suddenly Applejack using her own strength to stop the boulder. She kicked it all the way over the site, before stretching her hooves like it was nothing.

The Professor was flabbergasted, "I can't believe you just did that. Y-You saved us!"

Applejack answered, "I bet if you told somepony else the story, it might sound..." she mimicked a gasp, "Preposterous." Casey laughed at Applejack's quip.

One of the ponies motioned to where the boulder was and revealed a passage way, "Whoa. Check it." Casey gasped.

"I suppose some stories might be true..." The Professor admitted, as Applejack and Casey showed them the shovel they were looking for, as it began to glow, "And Rockhoof's appears to be one of them."

Casey and A.J walked out, as Casey spoke to his friend, "One artifact down, and four to go."

"Let's hope the others aren't having any trouble with theirs." Applejack said.

Meanwhile, Rarity, April, and Donnie wandered into a yard where the garden was filled with thick plants, "Where's a gardener when ya need one?" Donnie asked.

"It's like a jungle in here.' April added.

"Wait, look." Rarity pointed to a single bloomed flower in a pot.

"All right, we found it," Donnie reached to grab it, only for his hand to get whacked by a gardening tool, "Ow!" he cringed while holding his hand.

April and Rarity looked seeing an old unicorn mare who was using her magic to levitate the garden tool, "You keep those hooves to yourself, sonny! This place has been in my family for generations, and I'm not about to let some whippersnapper take the last good piece of it! Time was different back then, ponies came from far and wide to see these gardens. But that flower's the only worthwhile thing left!" she told them like a cranky old mare.

Rarity and April looked around, until they gained the same idea, "Don't be so sure about that, ma'am." April told her, as she and Rarity used their magic to do a little gardening.

Donnie and the elder pony looked around the new refreshed garden feeling stupefied. Rarity spoke up to the elder one, "Perhaps it just seemed like your gardens were worthless. But a little pruning can work wonders. Of course you will have to look after more than just one flower now."

The old pony smiled, with tears in her eyes, "You've given me back my family's legacy. The flower you wanted seems like a fair trade for that." she levitated the flower to them, as it began to glow.

"Thank you, ma'am. And trust me, your offer to us will may just help us help a lot more ponies." Donnie explained, as they took their leave, with the elder pony looking confused by what Donnie said.

Elsewhere, Rainbow Dash was carrying Raph on her back, while Spike was holding onto Raph's back. The three were currently flying around the Dragon Lands, "I can't believe Flash Magnus' shield ended up in the Dragon Lands." Rainbow said in disbelief.

Spike answered, "Good thing you brought the official Equestrian friendship ambassador to the dragons to help you navigate our customs. Like our favorite sport – gorge surfing!" The two looked down seeing dragons surfing on rocky platforms down a gorge of flowing lava.

"Whoa. Now that looks like a wicked sport." Raph admitted, as a dragon surfed down the lava before landing at the bottom perfectly.

Rainbow landed, "Ok, that was awesome."

The teen dragons turned to face them, as one spoke, "Dragon Lord Ember commanded us to make peace with ponies, but it doesn't mean you can surf in our spot." the dragons growled.

Raph drew his sais, "You scale heads wanna start something, because I'll finish it."

"Raph!" Spike stopped him, and approached the dragons to address them, "Whoa, fellas. As the official Equestrian friendship ambassador to the dragons, I have to say that's not very friendly."

Suddenly stepping out from the group of teen dragons was Spike's dragon rival Garble, "Well, what do you know? The puny pony-dragon's sticking up for his pony pal. If you even are a pony. I mean what pony walks on two legs?" Garble joked.

Raph growled, "A pony that's gonna rip your wings off!" he tried to go at Garble, only for Rainbow to spot Garble was holding Flash's shield.

"Hey! That's an ancient pony artifact!" She called, as Spike and Raph noticed it. Rainbow tried to take it only for Garble to push her back.

Garble held the shield close, "Hooves off my gorge board! I found it in the desert, and finders keepers."

"That is not yours, pal." Raph warned him.

"I'm not your pal, and it sure looks like mine. But I might consider racing you for it." Garble tempted him.

"You're on!" Raph accepted the challenge.

"Um... No. I mean... you." Garble motioned to Spike who got nervous.

"Oh, that's real fair. Picking a dragon smaller than you? You're just a coward!" Raph called him.

"Come over here and say that to my face, pony-freak!" Garble argued.

Raph growled, as he was once again ready to attack, until Spike came between them, "It's all right Raph. I accept the challenge." he told Garble

"Well, we're doomed." Raph said dryly, as Spike scowled.

Soon the two met at the top of the gorge, with Spike using a gorge board, and Garble using the shield. The two stood at the starting point with Rainbow and Raph smiling to Spike with support, while Garble just blew raspberry's at him in mockery. One dragon announced, "On your marks... Get set... Surf!" Spike and Garble took off surfing down the gorge of lava. Spike was doing good, until Garble surfed around him.

Spike started losing balance, as he slid off a rock shaped ramp. He hit various rocks on the way but still held onto his board. He hit the last rock and flew over Garble reaching the finish line before him, "Yeah!" Raph and Rainbow cheered.

Spike noticed he won, "I won? I won! Woo-hoo! Give up the shield, Garble!"

Garble put the shield on his back and answered, "Dragon Lord Ember only commanded us to be nice to ponies. She never said anything about pony-loving dragons." he stomped over to Spike who looked nervous.

"Uh, s-since Dragon Lord Ember commanded you to make peace with ponies, you can't very well attack one of their friends, can you?" Spike asked hopefully.

Garble picked up a rock with both hands, holding it above his head, "I guess we'll find out!" he was about to throw it, until he felt a tap on his shoulder from behind, "What?" he turned around and came face to face with Raph. The mutant threw a fist back before slugging Garble right in the face. The dragon fell on his back, and to add more to his injury the rock he held landed on his stomach making him groan.

"Bad sportsmanship will get you nothing," Raph said, as he took the shield from Garble and gave it to Rainbow Dash, making it glow. Raph turned to Spike, "You did good, Spike. Well done." the two slapped some skin.

"Come on, let's go." Spike said, as the three headed back.

In the Hayseed Swamp, a pony named Cattail was using a familiar mask to confuse some Flash Bees. He started leading them away from their hive, as Fluttershy whispered to him, "Just remember not to turn away from them, Cattail. Flash bees can get pretty aggressive. I guess that's why none of the other bayou animals can get to the water." she motioned to some small gators and snakes who wanted to get to the water.

Mikey who was with her and Blade, spoke, "I don't wanna get stung by bees. Reminds me of the mutant wasps." he shivered.

"Do I even wanna know?" Blade asked Mikey rhetorically.

Cattail spoke to Fluttershy, "Wouldn't it make more sense for you to wear the mask that calms the bees?"

"It would..." Fluttershy flew up the tree to the hive, "If I didn't have to fly up here to move their hive. There!" she placed it on another branch higher in the tree. Cattail jumped into the bush as the flash bees flew back up to their hive, "Now the other bayou creatures can get to the water without the bees feeling threatened." she finished, as the animals went to the water.

"You know, you didn't have to help with this. I would've lent you the mask anyway." Cattail reminded her, as he removed the mask.

Mikey answered, "We know, bra."

Fluttershy added, "But I couldn't leave without helping."

"Yes. Helping others is one of the best things we can do." Blade added.

Fluttershy accepted the mask that glowed, "Ooh, glowy." Mikey said feeling entranced.

Finally at the pyramid in Somnambula, Daring Do was with a few other ponies including Shini. One of the ponies spoke, "I don't think anypony can find anything in there." he motioned to the green bubbling slime below them.

Daring Do answered, "I wouldn't give up hope just yet."

"What she said." Shini agreed, as she was stepping on a foot pump.

Suddenly the slime started draining out and Pinkie popped out of the drain wearing a diving suit, and was holding something, "This old blindfold was stuck in the drain."

"Weren't you looking for a blindfold?" Daring asked.

"She's right, Pinkie." Shini confirmed.

"Oh, yeah." Pinkie remembered, as the blindfold glowed.

"Well, we have what we came for. It's time to go," Shini said, as she turned to Daring Do, "Thank you for helping us, Daring Do."

"Any friend of Rainbow Dash is worth helping." Daring stated. Shini smiled, as she left with Pinkie Pie.

Back at Ponhenge, Twilight, Starlight, Sunburst, Leo, and Karai were waiting for the others to return. Twilight voiced her excitement, "I can't believe I'm gonna meet Star Swirl the Bearded! You know, outside of my dreams."

"I can't believe you're actually going through with it." Starlight voiced her opinion.

"What do you mean?" Twilight asked in confusion.

"I'm all for pushing the envelope, obviously, but this is pretty out there for you, Twilight." Starlight explained.

Sunburst asked, "What's 'out there' about saving the most legendary ponies of all time from a thousands-year-old prison?"

"Well... nothing when you say it like that. Unless "the most legendary ponies of all time" knew what they were doing, and we shouldn't mess with it."

Karai spoke up, "I actually agree with Starlight. Isn't it best to just leave well enough alone instead of poking at it?"

Leo answered, "True, Karai. But I'm sure Star Swirl and the Pillars did the best they could back then, but magic has come a long way. Mostly because of the work they did."

"That's true. And Twilight did get her wings from finishing one of Star Swirl's spells." Starlight admitted.

"Exactly." Twilight nodded.

"But then I messed with one and nearly destroyed the universe, so..." Starlight trailed off, as Twilight spoke.

"Starlight, Star Swirl the Bearded is the greatest wizard who ever lived. The chance to have him back in Equestria is worth the risk."

"That's good news." Spike said, as everyone returned with the artifact they were sent to find.

"Otherwise, we'd have brought this shield for nothing." Rainbow held Flash's Shield, before placing it down before one of the rocks.

"I don't know, punching that dragon in the face was good enough." Raph said.

"I hope you don't think you're the only one to find her artifact, because this here shovel says otherwise." A.J placed Rockhoof's shovel in a spot.

"Score for us." Casey said, as he and Applejack high hoofed.

Rarity laughed, as she, April, and Donnie returned with the flower. The fashion pony spoke, "Honestly. Not everything is a competition. But Mistmane's flower is by far the most attractive of the artifacts." she placed the flower in its spot.

Pinkie returned with Shini, "You're just saying that because you didn't have to scuba dive in a pit of green slime to get yours!" Pinkie spoke.

"Better her than me." Shini replied.

Fluttershy came back with Mikey, and spoke, "Or move a flash beehive."

"All artifacts accounted for." Leo took count.

"Good work, everyone. Let's do this!" Twilight said, as she put Star Swirls' book in its original spot.

Twilight, Sunburst, Starlight, Shini, and April concentrated their unicorn magic onto the book. The book connected to the other artifacts forming a hexagon shape that levitated above them. In a flash of magic six ponies fell form the sky and landed by a pillar each. Each of the group grabbed one of the ponies before a rock almost crushed each of them.

Star Swirl opened his eyes and looked around, "What... What has happened?"

Twilight smiled, "It worked! We brought you back!"

"To where?" he wondered.

Leo spoke, "Well, sir, you and the others have been trapped in limbo for over a thousand years."

Twilight continued, "But I figured out how to get you ho-" she was cut off as Star Swirl began to panic.

"What?! No, no, no, no! You must undo what you've done!"

"Say what?" Raph asked.

"But we just got you back." Mikey noted.

"Why? I mean, I don't think I can." Twilight told the old wizard.

"You cannot bring us back!" he warned her.

"But I did. I brought all the Pillars back." Twilight replied.

"You cannot bring only the Pillars back!" Star Swirl said in worry.

"What are you talking about?" Karai asked, as lighting started striking around them.

"Is this part of the spell?" Casey asked.

"I don't think so." April said in worry.

Suddenly appearing before them was the Pony of Shadows who laughed evilly. Every pony was in shock, as Mikey spoke, "Dudes, I think we're in trouble here."

"Oh, no!" Twilight cried, realizing she made a grave mistake with her spell.

The Pony of Shadows

At first it started off like a good idea. A chance to release the legendary ponies from Limbo sounded like a once in a lifetime chance. But not everything turns out to be as easy as it sounds. That is what Princess Twilight and her friends learned the hard way. After releasing the pillars from Limbo, they unintentionally released the Pony of Shadows as well.

The dark pony laughed, "Your pitiful attempt to imprison me has failed, Star Swirl!"

Star Swirl tried to fire a blast of magic from his horn, but was too weak to cast it. He spoke to Twilight, "You must return us to limbo. It's the only way to stop him."

"I only figured out how to bring you back." Twilight answered.

"So let's try finding a way to undo it." Donnie suggested.

"Working on it." Sunburst started checking a book.

Donnie looked through it and groaned, "What good is a book without a table of contents?!"

"Allow me to assist," Pony of Shadows extended shadow spikes from his body piercing the book to one of the rocks, while the other spikes pierced the other five destroying all six formations, "There! Without the power of Ponhenge, your banishing spell is useless!"

Star Swirl turned to Twilight, "You have studied my writings. Surely you have some other plan."

"No. I just wanted to save you. I didn't think..."

The Pony of Shadows cut her off, "Don't fret. When I extinguish the light and hope of this miserable world, you won't remember any of this." he was about to blast them with his magic only for something to whack him in the face. He turned to see it was April who used her tessesn.

"Don't count on it." she warned him.

Leo drew his swords, and announced to his comrades, "Ninjas, take him down!" the ninjas jumped into battle along with Blade.

Each of them was striking at the shadow pony with their weapons distorting him. Casey flew up while bouncing explosive pucks off his goalie stick, "Let's see how ya like this. Goongala!" he swatted the explosive pucks at the Pony of Shadows, that exploded to distort his senses.

Blade jumped in while powering up his sword and sliced one of his enemies shadow tendrils, "Yes!" he pumped a fist only to see his enemy regenerating, "Oh, no."

"I don't know who you are, but you are an even bigger pestilence than those who trapped me!" The Pony of Shadows shouted, before blasting his magic at Leo.

"Leo, no!" Twilight jumped in and fired magic from her horn to counter the Pony of Shadows magic.

The evil pony recoiled before speaking, "This one is almost as... strong as you, Star Swirl. But even in my weakened state, she cannot stop the might of shadows!" he once again blasted Twilight with magic as she tried to hold him back with her own.

Suddenly Starlight jumped in lending Twilight her magic, "Lucky for her, she's not alone!" Starlight told the villain.

April joined in using her own magic with theirs, "And she never will be!" the three magic blasts overpowered the Pony of Shadows who backed off.

Star Swirl spoke to the creature, "Know this, fiend! We will not rest until we find a way to return you to limbo!"

The Pony of Shadows only growled, "Never! Your days of glory are through, Star Swirl. Now my dark power will reign, and you six will bow to me!" he turned to a cloud and went up to the sky taking the clouds with him, making the weather normal again.

"Where'd he go?" Shini asked.

Somnambula answered, "That is a riddle we must unravel. And quickly."

Meadowbrook asked Fluttershy and Mikey, "How long have we been gone."

"Over a thousand years." Fluttershy answered.

"Yeah. Long time we know." Mikey added.

"Then my spell worked," Star Swirl began, "Before it was meddled with and the realm has been at peace for a millennia!" he looked to Twilight with disappointment.

Leo came to her defense, "Give her a break, Star Swirl, like any of us would've known this was going to happen!"

"Yeah. You should've had better notes left over for any pony who may find them!" Raph added.

"Plus Bearded dude, Equestria wasn't always at peace since you left." Casey put in.

"It wasn't?" Rockhoof asked.

Pinkie spoke up, "Weeeeell... we did have to save everypony from Nightmare Moon and Discord and Chrysalis and King Sombra and Lord Tirek, and there was that one time when Starlight traveled through time and almost destroyed life as we know it! And Blade Swipe here tried to destroy us once before. But that's all in the past." Starlight and Blade smiled sheepishly at Star Swirl.

Flash Magnus spoke with confidence, "If you are truly this accomplished, we will stop the Pony of Shadows twice as fast together."

"Took the words out of my mouth." Mikey agreed.

"We shall see," Star Swirl began skeptically, "It is an easy thing to say you have saved the world. It is quite another to do it."

Leo spoke up, "If you knew what me and my comrades have done to save our world, you wouldn't sound so skeptical."

"Try me." Star Swirl replied.

Before Leo could speak, Mikey decided to answer, "We've fought monsters, mutants, alien brains and alien dinosaurs, ooh, there was also the time we fought iconic monsters from the past, and all sorts of messed up baddies."

"Incredible." Mistmane gasped.

"After witnessing how you fought, I can believe it." Flash Magnus admitted.

"But who are all of you?" Somnambula asked.

"I'm Leonardo."

"Michelangelo."

"Donatello."

"I'm Raphael."

"April O'Neil."

"Casey Jones."

"Karai."

"And I'm Shinigami."

Twilight spoke up, "I'm Princess Twilight Sparkle."

"Rarity, of course."

"Rainbow Dash the awesome flier of this century."

"Name's Applejack."

"Pinkie Pie!"

"Fluttershy."

"Starlight Glimmer."

"Sunburst."

"And I'm Spike."

"My name is Blade Swipe."

The pillars took notice of the four brothers and Blade's stature, "Ponies walking on their hind legs?" Meadowbrook asked.

"We really have been gone a long time." Rockhoof said.

"Actually, we're not your run of the mill ponies." Donnie admitted.

"Then what are you?" Flash Magnus asked.

Blade answered, "We're mutants."

"Mutants?" Somnambula asked.

"Yeah, it's a long story, but we don't have time to go into detail." Leo answered.

"He is correct," Star Swirl agreed, "Equestria's fate hangs in the balance. Saving it will not be an easy feat."

Rainbow spoke, "Oh, we've saved the world, Beardo. And we can do it again."

"It's what we do." Mikey added.

"Be that as it may, the problem of locating the Pony of Shadows remains, and this land is vast." Star Swirl noted.

Rarity spoke up, "It sounds like you need a map. Luckily, we have just the thing."

"Back to the castle." Blade instructed, as they all headed off.

As they walked or flew, Rockhoof looked at Casey, "That was an impressive move you pulled there, Casey."

"Really? Ya think?" he asked hopefully.

Rockhoof nodded, "That weapon you carry is just right for you."

"Thanks, but it's nowhere near as cool as that shovel of yours. I mean you dug a whole trench by yourself using it."

"I just did what I felt was right." Rockhoof admitted. Twilight watched feeling good for Casey to bond with one of the pillars, but just wish she left a better impression on Star Swirl.

Later back at Twilight's castle, the group was in the throne room looking at the cutie map. The pillars looked around as if they were feeling something familiar. Star Swirl spoke, "Something about this magic seems familiar..." he used his magic on the map projecting an image of the Tree of Harmony.

"What is that?" Karai asked.

"It's the Tree of Harmony." Twilight answered.

"Did you know he can do that?" Rarity asked Twilight.

"He's Star Swirl! He can do anything!" She answered with excitement.

Star Swirl spoke, "This map, and indeed this very castle, are grown from the seed we planted over a thousand years ago."

"Then it did work!" Rockhoof said proudly.

"What worked?" April asked.

Somnambula answered, "Each of us infused a crystal seed with our magic in hopes that it would grow into a force for good."

Mistmane continued, "We wanted to leave something to protect the realm in our absence, but we never dreamed our gift would become so powerful."

"Y'all mean the Elements came from you?" Applejack asked in disbelief.

"Fascinating." Donnie gasped, while the pillars were confused.

"The what now?" Flash Magnus asked in confusion.

Pinkie answered, "You know, the sparkly crystal things that grow from the Tree of Harmony and represent each of us? Laughter, honesty, generosity, loyalty, kindness, and magic!"

"Ring any bells in you now?" Raph inquired.

"They are reflections of our own elements of hope, strength, beauty, bravery, healing, and sorcery." Somnambula explained, while motioning to herself, Rockhoof, Mistmane, Flash Magnus, Meadowbrook, and Star Swirl. Each of the pillars and girls smiled at each other, while Star Swirl didn't even acknowledge Twilight.

"We had no idea our small seed would bloom into the living spirit of the land," Meadowbrook began, "I am glad our mantles have passed to such capable ponies."

Star Swirl spoke, "More importantly, we no longer need Ponhenge to send our foe back to limbo. We can use the stored magic in this Tree of Harmony."

"But doesn't a banishing spell take a lot of power?" Twilight asked, "We'd have to sacrifice the Elements for that."

"Correct." he confirmed.

"But the elements of harmony would be lost forever." Fluttershy gasped.

"Say it isn't so!" Mikey cried.

"Star Swirl, I don't think the Tree can survive without the Elements. If it dies, Equestria will suffer." Twilight pleaded with her mentor.

Blade spoke, "Twilight's right. It's too big of a risk."

Star Swirl answered, "If the Pony of Shadows has his way, your land will not exist. So unless you have a better idea..." he used his horn to return the map to normal and everyone saw dark clouds hanging over certain parts of Equestria, "Our foe will seek dark places from which to draw power. I will prepare my spell so that we may strike as soon as you find him."

"Well, what're we waiting for?" Rainbow asked.

"Let's go find us a shadow pony." Casey added.

Flash spoke to the two, "I like your spirits."

"Indeed." Rockhoof agreed. As everyone got excited, Twilight left sulking, which didn't go unnoticed by Starlight, Leo, and Karai.

The three walked through the halls, as Starlight spoke, "I feel bad for Twilight."

"Me too, even if Twilight didn't think things all the way through, none of us could've seen this coming." Leo added.

"Apparently Star Swirl doesn't believe in mistakes." Karai noted, as they reached the library to see Twilight panicking.

"Twi, are you ok?" Leo asked.

"I just unleashed ultimate evil and doomed Equestria because I was obsessed with meeting my idol! Why wouldn't I be okay?!" Twilight asked, before dropping her head on the table.

Starlight scoffed, "You didn't know that was gonna happen."

"None of us did." Karai added.

"But I should have listened to you and left things alone. Now the Elements of Harmony will be lost to fix my mistake!" Twilight continued to crack.

"Maybe there's another way." Starlight suggested.

"There's always another way." Leo confirmed.

"If there is Twilight will find it." Spike said, as he carried a stack of books.

Twilight checked a book, "Portal gate... Portal keys... Portal spells... Yes! If the Pillars can hold open the gateway to limbo, a powerful pony can do the banishing spell herself! Do you know what this means?"

"I can stop carrying books?" Spike asked, while panting.

Twilight explained her plan, "The Pillars don't have to leave Equestria! Even though we'll lose the Elements, we'll have the ponies that created them. And the Pony of Shadows will be banished for good!"

The three looked uneasy, as Starlight asked, "Great, but I was thinking of another way that maybe doesn't involve banishing at all?"

"Yeah, I thought we could find another way." Leo agreed.

"Guys, Star Swirl knew what he was doing when he cast that spell. If I can make it even better, maybe he'll see that I take magic as seriously as he does." Twilight said with hope.

Karai spoke, "I don't think trying to impress him is all worth it."

"What?" Twilight gasped, "How can you say that, Karai?"

"I mean you no disrespect, Twilight, but ever since he got here all he's been doing is behaving like everyone is below him and that he doesn't care what he does as long as he gets his way. It's just like being around Shredder."

"Karai, that is a horrible thing to say!" Twilight snapped, "Star Swirl is not like Shredder. He stopped the Pony of Shadows from conquering Equestria."

"Well, listening to him talk about banishment like it's a normal thing rubs me the wrong way." Karai argued.

Starlight and Leo came between them, "Girls, come on, this is no time to start arguing." Leo warned them.

"Leo's right. We start fighting each other, we'll get nowhere." Starlight added.

Twilight and Karai looked at each other and sighed, "I'm sorry, Twilight." Karai apologized.

"I'm sorry too, Karai." Twilight replied, as the embraced.

"Hey, we're back!" Came Mikey's voice.

The five returned to the throne room to see the others, "Did you find anything?" Leo asked his brothers.

"Zilch." Raph answered.

"All the potential places Star Swirl predicted where The Pony of Shadows would go don't appear to be suited for him." Donnie explained.

Star Swirl spoke, "It seems there are fewer dark corners in the realm these days."

"Isn't that a good thing?" Mikey asked.

"True. The Pony of Shadows will have a hard time regaining power," Flash admitted, "When he rears his head, we'll be ready!"

"You bet we will." Casey agreed.

"Isn't there some way to banish him without losing all of you?" Fluttershy asked.

"Yeah, anything at all?" April wondered.

Meadowbrook answered, "Oh, I wish there were. But to save our home, we are willin' to leave it."

"I don't think you'll have to," Twilight answered, as she came in carrying a scroll, "My spell isn't finished yet, but I think we can send the Pony of Shadows to limbo without all of you having to go as well!"

Star Swirl brushed it off, "While I appreciate your enthusiasm, Twilight, this is hardly the time to take risks on half-baked spells."

Twilight sighed, only for Leo to once again come to her aid, "Twilight doesn't do anything half way."

"Especially not magic!" Pinkie added.

"Seriously! She got her wings by finishing one of your spells!" Rainbow Dash clarified.

"And that calls for something." Raph agreed.

"I think you'll find her work is worth reading before you dismiss it out of hoof!" Rarity insisted.

"That's right." Shini agreed, as the others stuck by Twilight's side.

Meadowbrook looked the spell over, "While it is an unconventional approach, I believe it could work."

Star Swirl looked it over, "Hmm. I suppose there is a chance."

"Of course there is," Leo replied, "As long as our hearts still beat and are willing to keep fighting, there's always a chance."

"But we still have no idea where to find the villain." Sunburst reminded them.

"At times like this I wish we had a sign." Mikey sighed, until the cutie marks of Twilight and the girls began to shine and went to a spot on the map.

"Maybe we should try there?" Spike suggested.

"Where is there?" Karai asked.

Applejack answered, "The Hollow Shades. I think a branch of the Apple family lives there."

"They'd have to be pretty distant. The Hollow Shades was abandoned eons ago." Sunburst noted.

"Sounds like the perfect place for a shadow pony." Blade added.

"Hmm, that's odd. The only time the map's called all of us to one place was Starlight's village." Rarity recalled.

"So it's like a super-villain tracker! No offense." Rainbow told Starlight, who raised a brow feeling irritated.

Twilight spoke to Star Swirl, "Do you think the map could be trying to tell us where the Pony of Shadows is?"

"Hmm... The Tree of Harmony acting to protect the light of the realm... Yes. A good thought, Twilight," he confirmed, as Twilight squealed having finally gotten a bit of recognition from her idol, "I will make my notes on this spell. Ready yourselves for battle."

Starlight spoke up, "Uh, I know I'm not as experienced as all of you, but is banishment really the only option? I mean, it's been a long time. Maybe the Pony of Shadows is ready to talk?"

Star Swirl answered, "I doubt we can save our homeland with a conversation."

"Well, we can still try." Karai argued.

Twilight spoke to the two, "Karai, Starlight, I'm sure Star Swirl and the others did try."

However, Star Swirl had a different answer, "The Pony of Shadows was not interested in reconciliation. Once a villain, always a villain."

At the sound of that, the turtle/pony ninja, and their friends gasped. Karai frowned, "What did you say?"

"Must I repeat myself, child?" Star Swirl asked rhetorically.

"Once a villain, always a villain?" she repeated him sounding angrier, which her friends knew was not sitting well with her, "Is that how you view all villains? What about somepony who was taken from her father by another pretending to be her birth father and raised her to believe that her birth father was her enemy. Is it her fault for that?!" she hissed as her eyes turned into her snake ones, and her snake fangs grew.

Star Swirl was taken aback by this, until Leo jumped in and broke them up, "Karai, enough! He's not worth it!" Karai with much reluctance backed down and turned away from Star Swirl. Leo turned to the wizard and spoke equally angry, "I don't know what you were raised to believe, but know this even a villain is more than capable of changing."

Blade stood by Leo's side, "I can vouch for Leo on this."

"I hate to break up this spat, but we got important things to deal with now." Donnie said.

Star Swirl answered, "Correct. Twilight, Sunburst, Donatello, would you accompany me? I wish to refine this spell for our use." he said, as the three followed him.

"Come. We must prepare for the struggle ahead." Rockhoof said, as they left the throne room.

Starlight and Karai sighed, as Spike spoke, "Don't listen to him. He just doesn't know the kind of ponies you really are."

"Thanks, Spike," Karai replied, "I just can't believe Twilight would idolize somepony like him."

"Star Swirl is a great wizard, but this whole plan seems... wrong. The map's only ever sent us to solve friendship problems." Starlight added.

"Maybe so, but the Pony of Shadows doesn't really seem like the "friendship" type." Spike replied.

"We don't know that for sure." Karai noted.

"Well, nopony does." Spike reminded them.

Starlight and Karai lit up as an idea came to mind, "Actually, there might be." Starlight said.

"The Pillars have to know about him, so let's ask." Karai suggested, as they went to talk to them.

Meanwhile the pillars, and the ninjas were preparing themselves for battle, until the two former baddies approached, "A moment of your time, honored ones." Karai inquired.

"Certainly, Karai." Meadowbrook replied.

"You all knew the Pony of Shadows before he became what he is now," Starlight began, "You must've been friends. So what happened?"

"Yeah, how did he come to be?" April wondered herself.

The Pillars looked at each other uneasy, as Rockhoof began, "The tale of our rift is a sad one."

"We've heard plenty of sad and tragic tales ourselves." Mikey admitted.

The Pillars flashed back a thousand years ago, when the Dazzlings who were just sirens used their hypnotic voices to spread disharmony across Equestria so they could feed on it.

Rockhoof narrated, "Stygian was a pony like the rest of us, though more scholar than hero. He recognized our emerging world would need champions to defend it." After the pillars banished the Dazzlings through the portal, the pillars were being praised, while Stygian was left in the dust.

Flash Magnus narrated a bit, "He may have gathered us together, but he himself was just an ordinary unicorn who soon grew jealous of our abilities."

"He stole objects from each of us. Artifacts to use in a spell." Mistmane narrated.

"And we cast him out for it." Meadowbrook added.

Somnambula finished, "We always thought he'd return and seek forgiveness. But when we saw him again, his heart was bent on revenge. He dashed even my hope of saving him."

"But why would he do that in the first place?" Karai asked.

"No doubt it was an enchantment to take our powers for himself." Meadowbrook believed.

"So you just banished him without even hearing him out?" Starlight asked.

"It was Star Swirl's order." Rockhoof answered.

"There's a surprise." Raph replied dryly.

"Looks like we'll have to get answers out of him now." Starlight said.

"Agreed." Karai nodded, as they went to talk to him.

In the library, Star Swirl, and the three eggheads were busy refining the spell of Twilight's, as Donnie spoke, "So if you do it like that it will work." Donnie finished.

Star Swirl spoke, "You have a brilliant mind, Donatello. Such a shame you're not a unicorn. You could really perfect various spells."

Donnie looked excited, but saw Twilight looking dismal for not being as commended, "You give me too much credit Star Swirl. Besides my intelligence is better suited for science, not magic."

Starlight and Karai came in and noticed all the books, "That looks like a lot of work." Starlight began.

"It is what must be done, and it would be best if we were not disturbed." Star Swirl answered.

"Rude much?" Karai asked.

Twilight spoke, "I'm sorry, but we can't stop to talk. The stakes are too high, and we have to..."

"Banish Stygian to limbo. We get it." Starlight replied.

"Who?" Sunburst asked.

"Who's Stygian?" Donnie asked.

"Stygian was the name the Pony of Shadows gave up when he turned to darkness." Star Swirl explained.

"And we're just trying to figure out why." Starlight noted.

"Envy," Star Swirl replied, "He wanted more power than he had, and that desire led him down a path from which there is no return!"

Karai frowned, "So says you!"

"I know from experience that's not always true," Starlight added, before turning to Twilight, "When the map called you six to my village, it was for a friendship problem. Are you sure this is different?"

Before Twilight could say anything, Star Swirl spoke, "Stygian wants to destroy all that is good in this world. There's no way to befriend a pony like that." he walked away.

Both Starlight and Karai looked more hurt than before. Starlight spoke to Twilight in tears, "I guess I'm lucky your idol wasn't around when you decided to be my friend. I might've been banished to limbo, too." she left.

Karai spoke to the Princess, "Is your idol still as cracked up to be as you thought? Like I said, being around him is no different than being around Shredder." she went after Starlight leaving Twilight second guessing everything.

Donnie spoke, "I actually agree with them. All this talk of banishment seems to the be the only method Star Swirl knew. But we're different from him. We have our own ways."

"I know, Donnie, but right now this is our best option." Twilight replied.

"If you say so." Donnie replied, as they left the library.

The group walked up to the Tree of Harmony, with the ninjas and pillars looking amazed, "Wow, pretty." Mikey gasped.

"It's beautiful." April added.

"Amazing." Shini put in.

"So those are the elements of harmony?" Donnie asked.

"Indeed." Rarity confirmed.

Somnambula spoke in nostalgia, "I am glad we have the chance to see what has grown from our efforts so long ago."

"It seems a shame to harm it." Mistmane said in guilt.

"A necessary sacrifice," Star Swirl began, "With the Elements' power, we will bind the Pony of Shadows in limbo. And thanks to Twilight, we will remain to watch over the realm ourselves." he used his magic on the elements as they became necklaces for the five girls, and Twilight's former crown.

"So how do we use them?" Rockhoof asked.

"Yeah, how?" Casey wondered.

"Well, you... Oh. I'm not sure. They simply work for us." Rarity answered also feeling unsure.

"This is why they should make instruction manuals." Mikey said.

Star Swirl spoke to the girls, "The Elements are attuned to you. We must use their magic in pairs."

"No problem, we're used to banishing evil before breakfast." Rainbow boasted.

"And it'll be an honor to save Equestria with ya'll." Applejack added.

Leo stepped forward and put his hand out, "Alright team. This is for Equestria. We will fight to protect it."

His friends put their hands or hoofs on top of his before the girls, Sunburst, and Starlight put their hoofs on theirs. The pillars each put their own hooves in while Star Swirl stood off to the side, "Star Swirl, are you with us?" Leo asked.

The ponies looked to him, as he tried to remain indifferent, before reluctantly putting his hoof on top. This act made them happy, as they broke, "Alright, onward to the Hollow Shades!" Mikey cheered, as they set out.

Starlight spoke to Karai, "I hope Twilight knows what she's doing."

"You and me both." Karai agreed, as they followed.

They arrived at the Hollow Shades seeing a red sky above it, "I don't remember reading anything that said the Hollow Shades was like this." Sunburst noted.

"Looks like our shadow friend was here already." Raph deduced.

Mistmane spoke, "Raphael is right, the Pony of Shadows must have twisted it to his purposes."

"So it's up to us to change it back." Leo said.

They stopped to hear a familiar evil laugh. April concentrated, "He's here all right." she said.

"Prepare yourselves," Star Swirl instructed everyone, "Stygian! Show yourself and face us!"

The Pony of Shadows' laugh echoed around them, as the ground started cracking, "Oops." Mikey said, as the ground caved in, and they fell through a hole.

They landed in a pile before picking themselves up, "Wipe out." Mikey groaned.

"Where are we?" Casey asked, as they looked around seeing they were in a hidden chamber that was dedicated to the Pony of Shadow.

"Freaky." Raph said.

Sunburst spoke, "I definitely would've remembered reading about this."

The Pony of Shadows' laugh continued to echo, as Star Swirl provided a protection spell around them. The dark pony appeared, and spoke, "Welcome to the Well of Shade! When you turned your backs on me, I discovered this place. The darkness spoke to me of a power beyond any I could imagine, and I listened. The shadow and I became one. Soon, all of the realm will be the same. Then all ponies will feel the despair I did when you cast me out!" he called the pillars out.

"We did what we had to do. You tried to steal our powers for yourself." Star Swirl accused him.

"No! It was you who were selfish! And now you will pay!" The Pony of Shadow concentrated his dark magic, and appearing on the floor were multiple miniature versions of himself in anthro form.

"They look like Dusk Ninjas." Donnie gasped.

"Only badder." Mikey said.

April used her magic to make an opening in the barrier allowing the ninjas to get out, "Alright, team, let's take them!" Leo ordered.

"Booyakasha!" Mikey shouted, as the ninjas went into battle.

Leo and Blade using their skills with the sword tag teamed against some of the smaller shadow ponies slicing them and they evaporated into clouds.

"Come and get some!" Raph said, as he plowed through some of the shadow ponies.

Donnie used his bo-staff to trip some of the minions up, before stabbing one with the spear part. April using both her tessen and tanto was able to subdue some of the shadow ponies. Casey flew in whacking some of the minions with his baseball bat.

Mikey and Shini jumped around before lassoing up some of the mini pony of shadows with their chain weapons before throwing them into a wall. Karai was using her own blade against some ponies, until Spike called out, "Karai, behind you!"

Karai shifted into her snake form and dodged three shadow ponies, before using her serpent strikes at them. She shifted back to pony form before smirking at Star Swirl to give him a hint.

Starlight spoke to Twilight, "Are you still sure this isn't a friendship problem?" Twilight was second guessing herself, until Star Swirl ordered.

"Ready? Open the portal... Now!" the barrier broke, as the girls used the elements of harmony combined with the pillars artifacts to open the portal to Limbo. The portal began assimilating the villain, while they tried pushing him into it.

"No!" The Pony of Shadows cried, "You will not trap me again!"

"Twilight! Push him in!" Star Swirl ordered.

Twilight was about to use her magic to help, until she saw a normal pony trying to pull himself out of the Pony of Shadows. She could tell it was a unicorn, with short mane colored moderate cerulean and arctic blue, eyes colored brilliant azure, and his coat was medium gray, "There's a pony in there."

"What?" the ninjas gasped.

Twilight flew into the shadow, and found herself wandering in darkness she used her horn to provide light, and saw the pony, "Are you... Stygian?" she asked.

"I was once," he began, "Until my friends betrayed me."

"But Star Swirl says you betrayed them. You wanted their magic..." Twilight told him.

Stygian answered, "No! I wanted their respect. I brought them together. I planned strategy, and I read all I could about the beasts we faced. But I didn't have magic or strength, so nopony ever noticed me. I went to Ponhenge to make my own copies of the artifacts. With them, I thought I could be a Pillar, too, and stand by their side in battle. I never wanted to steal their power," As Stygian explained, all the ponies on the outside overheard him, and the pillars realized they made a mistake in judging him, "But instead of sharing and letting me help, my friends threw me out," his voice grew deeper and he growled, "So I became stronger than any of them! The darkness welcomed me when no pony would, and I will do what I must to protect it!" shadow surrounded Stygian and his eyes turned full white.

Twilight tried to reason, "This is all a misunderstanding! If the Pillars knew how you felt, I'm sure they wouldn't have turned their backs on you. The shadow isn't who you really are. Let me help you be Stygian again."

"Even if my friends did still care, what makes you think you have the power to help me?" Stygian asked with skepticism.

"Because it's what she does." Karai answered, as she and Starlight appeared in the darkness.

Starlight spoke, "I wasn't so different from you, and Twilight helped me change. If there's one pony in Equestria that can save a friendship, it's her."

"And I met a group of others who taught me a similar lesson." Karai added.

Stygian felt touched by their words, but strained, "I... I want to believe you... But the darkness will not be stopped!" he repelled the three, as the shadows started surrounding him.

"We have to get him out of here." Karai told Twilight.

The Princess used her magic to wrap a lasso around Stygian's hoof. The three ponies jumped out of the shadow and tried pulling him out, "Fight the darkness, Stygian! You don't need it anymore! Revenge isn't what you want! Friendship is!" she started losing her grip on Stygian.

"Twilight!" Starlight called, as she used her magic to help pull Stygian out. The shadow roared as it struggled.

"The shadow won't let go of him. He wants to stop, but he can't do it alone." Karai told the pillars.

"Then we must help him!" Star Swirl declared, as he, Blade Swipe, and Sunburst used their magic to help the two followed by April and Shini.

The others used the power of the elements to provide additional help to Stygian, with their combined efforts, they tugged Stygian out of the the shadow that was sent through the portal, "NO!" the shadow cried, as the portal closed trapping it.

Without the Pony of Shadows, its dark magic was extinguished allowing the sun to shine down on Hollow Shades. Every pony climbed or flew out of the hole. Rainbow cheered, "Yeah! Oh, it felt sooooo good to do that again!"

"Friendship power rush! WHOO!" Pinkie bounced.

"We're the best!" Mikey danced, "Go Ninja! Go Ninja! Go!"

Rarity noticed they still has the elements, "The Elements! They didn't disappear!"

"Maybe because we used them for healing magic instead of banishing?" Fluttershy asked.

"Affirmative, Fluttershy." Donnie agreed.

"Look." Leo motioned to Star Swirl who helped Stygian out of the pit.

The old pony had something to say to the young one, "Long ago, you needed our help, Stygian. But instead of listening, we turned our backs on you. Pride clouded my judgment. I owe you an apology," he turned to Twilight, "Thank you for helping us see the errors of our ways, Twilight. It seems I never accounted for the Magic of Friendship."

Twilight smiled, "Thank you, Swirlstar! Uh, Star Swirl!" the girls noticed their cutie marks glow meaning their friendship mission was a success.

"Looks like that's it for this mission." April said.

Starlight and Karai cleared their throats, "Soooo... apparently a conversation can save Equestria?" Starlight teased.

Star Swirl could only chuckle knowing he was proved wrong, "Something tells me I will be making a lot of apologies today."

"Well, you know who you can start with after Stygian." Leo told him.

Star Swirl turned to Starlight and Karai, "I am deeply sorry for what I said to the two of you. I've been so clouded by judgment and pride it never did occur to me that anypony can change if given the chance to."

"Thank you, sir." Starlight smiled.

"And I'll have you know something, Star Swirl," Karai began, "Those sirens you banished? They changed as well, and they now work for me."

Star Swirl was shocked, before speaking, "These truly are different times." the group laughed.

Aftermath

After all was done, the group of friends returned to Canterlot, where Star Swirl was overjoyed to see his two oldest pupils from so long ago, "I simply cannot believe how tall you've gotten!" he spoke to Celestia, as he looked up at her.

Celestia smiled in amusement, "Well, it has been over a thousand years. Will you stay here and teach magic once again? My sister and I have such fond memories of your lessons."

"As long as you don't ask for those essays we owed you before you disappeared." Luna said sheepishly, as the two sisters smiled.

Star Swirl chuckled, "I'm not certain Canterlot is where I belong. The realm has grown, and I believe I'll have a look around before I settle in any one place."

"And I long to see what has become of my home." Meadowbrook added.

"I believe we all do." Mistmane agreed.

Celestia spoke, "Then I hope you will return to Canterlot on occasion and share the wisdom of your great experience with the next generation of ponies."

"We would be honored. But if it is wisdom you seek, look no further than your own pupil," Star Swirl motioned to Twilight who smiled, "She showed me that the power of friendship is a magical force indeed. And that in turning away from others, you hurt yourself as well." the whole group gathered around Stygian for a group hug.

Twilight spoke to Starlight, "It's funny. I thought meeting my idol would give me all the answers I ever wanted. But instead, I forgot what I already knew. Good thing I had a student of my own to remind me." the two embraced before joining the others.

Later on in the Royal dining hall, the pillars were seated with the girls and the ninjas, as Mikey, Pinkie, and Blade came in carrying pizza boxes, "Hope you legendary ponies are ready to sample the greatest food this century." Mikey said.

"Yeah," Flash Magnus agreed, "After being stuck in Limbo for so long, I'd like to see what's all the rage today."

"We present to you... Pizza!" Mikey unveiled the food.

The legendary ponies each took a slice and had a bite of it. Each of their eyes lit up in wonder. Rockhoof was the first to react, "This is some delicious stuff."

"Better than the slop we had to eat during training." Flash added.

"Cheese, tomato sauce, and dough mixed together?" Star Swirl asked, "What an astonishing creation."

"Quite so." Meadowbrook agreed.

"We had nothing like this back in our time." Somnambula noted.

"Indeed. We missed out on so much." Mistmane finished.

Stygian spoke to Leo, "So, Leonardo, what did you and your brothers say you were again?"

"Mutants." he answered.

"And how did you become mutants?" Flash Magnus asked.

"Well, my brothers and friends are actually from another world." Leo began.

"And in our world we're actually mutant turtles." Donnie added.

"Turtles?" Meadowbrook asked.

"That's right. We became mutants through an unstable substance called mutagen." Donnie put in.

"Same for me, except Equestria is my birth home." Blade added.

"Where did this mutagen come from?" Somnambula asked.

"From an alien race known as the Kraang." Leo answered.

At the sound of that, Star Swirl gasped, and squinted his eyes, "Did you say 'The Kraang'?'

"Uh, yeah." Leo answered, feeling confused.

"Star Swirl, is something wrong?" Twilight asked.

"Forgive me, but I haven't heard that word in a long time." he replied.

"Wait a minute. Star Swirl, you know about the Kraang?" Donnie asked, as the group was surprised.

"Yes. I even met their leader a long time ago." Star Swirl used his magic to cast a flashback for everyone to see.

He began to narrate, "Over a thousand years ago before we banished the Pony of Shadows, I was given an invite by a being not of this dimension. A being known as Kraang Prime. He sought audience with me to discuss important matters. I wanted to see what those matters were."

Everyone watched as past Star Swirl came upon a hill side where three Kraang droids stood in position. The androids were modeled like ponies due to the laws of their dimension, while the Kraang themselves remained the same. The androids opened up a very large portable portal, and rising up from it was Kraang Prime on a hover platform. The large brain alien hovered above smiling evilly.

"Kraang Prime, I presume?" Star Swirl inquired.

"One called Star Swirl the Bearded," Kraang Prime addressed him, "Kraang has come with a most opportunistic offer for you."

"I'm listening." Star Swirl answered, as Kraang Prime continued.

"The land known as Equestria is rich with life and magic. But it could use some improvements."

"What sort of improvements?" the wizard raised a brow.

"Kraang has been experimenting on a substance called mutagen," Prime began, "With it, Kraang can terraform this land into an environment fit for all Kraang. And in return, Star Swirl the Bearded will have access to all of Kraang's technology."

Star Swirl squinted his eyes, seeing past the deception in the alien's words, and answered, "I'm sorry, but Equestria is not just a land for you to terraform just to suit your own purpose. I deny your offer."

Kraang Prime frowned, "If Star Swirl the Bearded will not join Kraang, then Kraang will destroy!" he bellowed, as the three droids stood on their hind legs and started blasting at Star Swirl.

The wizard used his magic to shield himself before blasting at the androids disarming them. He then used his power to levitate the droids and Kraang Prime pushing them down into the portal. Kraang Prime screeched as he and his three followers went through the portal that closed up. Star Swirl blasted the portable portal device so that they would not return.

Star Swirl narrated, as they watched the flashback shift, "It wasn't long after I was visited by the Utrom Council's ambassador Bishop," they saw Star Swirl meeting with their allie Bishop whose body was in pony form, "He promised me the Council would do what it took to keep the Kraang from ever trying to return to Equestria."

"Well, there's never been any other reporting of Kraang in Equestria." Luna assured him.

"Then the Utrom kept their word." Star Swirl smiled.

"Yeah, good for you," Raph began, "But then they decided to come to our world."

"If the Kraang continued to stick around in Equestria, there's no doubt the Triceratons would've found them and try to wipe out Equestria using the Heart of Darkness." Twilight shivered at the thought.

"Luckily those guys are finished." Spike reminded her.

"I wouldn't wanna get caught up in anything Kraang related for sure," Blade Swipe agreed, "But Star Swirl, there is something I want to know."

"What is it, Blade?" he wondered.

"What happened in the battle between you and Dark Codex?"

Star Swirl and Mistmane were surprised, "How do you know of Dark Codex?" Mistmane asked.

"Because he mind molded me into becoming bent on hating ponykind for casting me out because of how I looked after my mutation." Blade answered.

"Yeah. He said you two clashed a long time ago." April recalled.

Mistmane spoke, "That he did, but Dark Codex was actually a part of my kingdom."

"He was?" Rarity asked.

The old pony nodded, "Dark Codex was once a royal sorcerer to my friend Sable Spirit, but he was banished when he attempted to take over the throne."

Star Swirl continued, "He sought me out for my power so he could try and take over Mistmane's village. We clashed in our magic arts, but in the end I succeeded and trapped him inside his own grimmoire."

Stygian spoke up, "I was tasked with hiding it where nopony could ever find it. I'm guessing it didn't work?"

"Not so much," Blade admitted, "But it's all right. Dark Codex is no more. Thanks to my friends." he smiled at the group of ninjas.

Star Swirl stood up, "You lot have proven to be very loyal and dedicated ponies just as the inheritors of our mantles. So it is with great pride I bestow upon each of you your own mantle," he motioned to Leo, "Leadership!" he looked to Donnie, "Intelligence!" he eyed Raph, "Brawn!" he turned to Mikey, "Heart!" he looked at April, "Sympathy!" he looked to Casey, "Avenger!" he turned to Shini, "Trickery!" he finally looked to Karai, "And Justice!"

The group smiled, liking the titles Star Swirl bestowed on them. Leo spoke, as they bowed their heads to him, "Thank you, Star Swirl."

After their party, Twilight spoke to the ninjas, "Well, looks like it's time to send you guys home."

"We know." Leo confirmed.

"It was great seeing you all again." April told them.

"Likewise." Applejack agreed.

"Come back any time." Rainbow told them.

"You bet." Casey confirmed.

"And Star Swirl, if you and your pals ever wanna explore someplace new, you should come to our city. Just let us know ahead of time." Mikey suggested.

"Sounds good to us." Star Swirl smiled, as the others agreed.

Twilight and Starlight used their combined magic to open a portal back to their world. The ninjas looked through the portal seeing their home, "It's the lair!" Donnie gasped.

"Come on, team. Let's go home." Leo said, until Twilight trotted over and kissed him.

"For the road." She told him.

"Thanks." Leo blushed, as Raph and Karai dragged him through the portal with the rest of them.

The portal closed, as the ninjas were back in the lair, "Well, that was fun." Raph admitted.

"We just made history in Equestria." April added.

"Bet we'll be legends too." Mikey said.

"Whatever the case, I'm glad we could help our friends." Leo smiled.

Karai spoke, "I'll bet Twilight's gonna get started in writing this to Sunset Shimmer."

"She's gonna be shocked to hear that." Mikey chuckled.

"And be jealous she missed out on it." Shini giggled.

"Well, it's not like nothing exciting ever happens here or with her and the others." Raph noted. The group agreed, as they decided to kick back and relax knowing they earned their time of relaxation.

Author's Note

And there you have it, folks. The idea of Dark Codex the OC villain from Turtles of Equestria being involved in Mistmane's village was an extra backstory thought up by jebens1