Equestria Wars Episode IV: Shadows of Equestria

by sonicdash123

Rating: teen
Tags: Other, Romance, Original Character, Science Fiction, Starswirl the Bearded, Adventure, Crossover, Twilight Sparkle, Main 6, My Little Pony: Friendship is Magic, Dark, Alternate Universe
Length: 8488

After the second Death Star was destroyed, peace finally came to Equestria. A new foe now rises from the shadows and Charming Thunder and Twilight must work together to save the balance of Equestria.

When the Lunar Republic fell and the Death Star was once again destroyed, peace came to Equestria and an empire was finally born. Three months passed as a new foe rises from the shadows. Join the further adventures as Charming Thunder and Twilight work together to restore balance to Equestria. Discover the mystery of Charming Thunder's past as he meets Star Swirl the Bearded.

(Event before the Season 4 finale)

Published 2014-05-04 18:10:04 UTC
Last updated 2014-05-12 19:47:04 UTC

Chapter 1: Dreams

Charming Thunder's TIE Advanced arrived at the Crystal Empire and landed at a platform where Princess Cadence met up with him. As he exited the ship, he ran up to his sister and gave her a hug. "Its good to see you again, Cadence," Charming Thunder said.

"The pleasure's all mine," Cadence replied. "How's Twilight?"

"She's fine. We just settled at a house in Canterlot."

"Thats great news. I'll come visit some time."

"I just got your message that you found something relating to my father, correct?"

"Yes. Follow me." Charming Thunder followed Cadence through the hall and through a door to an ancient catacombs in the castle of the Crystal Empire. The room was full of boxes including a picture of a photograph of Sombra wearing a hat with bells on it, standing next to a young bearded unicorn at what looked like the Crystal Fair.

"Hm? Whats this?" Charming Thunder asked himself as he picked up the photo.

“What is it?” His sister asked walking over to him.

“It’s a photo of Sombra at the Crystal Fair standing next to somepony.” He said showing her the photo.

“No way, that’s Star Swirl the bearded!” The pink alicorn said a little surprised.

“Wait my Father was friends with Star Swirl?!” Charming Thunder said astounded.

“Looks like it.” Charming Thunder then placed the photo back where he found it and walked up to one of the boxes.

“So this is all my father’s old stuff?" he asked as he opened one of the boxes up to see what is in it.

“What’s left of it anyway.” Cadence said looking around. “All records of your father before he took over the Crystal Empire has been lost so if you want to find out anything about him during that time this would be the place to start.” Charming Thunder noticed another picture in the box. He picked it up and took a look at it. It was a picture of King Sombra with a cyan colored alicorn holding a wrapped up red filly.

"This must be...a picture of him and what seems to be my mother." He then showed it to Cadence. "She was in one of my dreams I keep having. Do you know who she is?"

"No. But I think that Celestia might." He then puts the picture back in the box ind closed it.

"Can you let some of your guards deliver these boxes to my home at Canterlot? I would appreciate it."

"Of course. I'll tell the guards immediately as you leave."

"Thanks. Your the best sister that I ever had." He then hugged Cadence and grabbed the photo of Sombra with Star Swirl and walked back to his ship.

As the massive fleet of Star Destroyers fly over Canterlot, Charming Thunder landed his fighter in a docking bay that was close to his home and exited to his house. When he entered the house, he saw his wife reading a book until she noticed him come in. "Hey, dear," Twilight said as she walked up to him and gave him a kiss on the cheek. "How was your visit at the Crystal Empire?"

"It was great," Charming Thunder said nudging her. "I have something special to show you." He then opened his saddlebag and levitated the photograph.

"What is it?"

"Its a picture of my father with a legendary unicorn; Star Swirl the Bearded." Twilight was surprised when she saw the picture.

"WOW! I didn't know your father was friends with him. Now I know what he really looks like."

Charming Thunder then placed the picture next to his wedding photo as he said, "There is more to it. Cadence's royal guards are bringing over boxes of stuff that was from my father's past life. They should be here any moment." A knock was heard at the door. "That must be them now." He then opened the door and the crystal pony guard was present.

"Where would you like us to put the boxes?" the guard asked as the others unloaded the boxes.

"You can put them in my room." The guards then carried the boxes upstairs to his room. "Would you like to help me unbox these, Twilight?"

"Of course."

Twilight was with Charming Thunder helping him unpacking the boxes. Charming Thunder took out the picture of his family and took a long look at it. "What is it, Charming Thunder?" Twilight asked.

"Nothing," he replied. "Its just...I wonder if my mother is still around. I never met her before now I know what she looks like." He then showed the photo he was holding to Twilight. "Cadence said that Celestia might know who she is."

"There's another princess? I didn't know there was another princess in Equestria. None of the books I read never mentioned her in it."

"Maybe tomorrow we can visit Celestia and ask her. In the meantime, why don't we wrap up. I'm starting to get tired."

"Yeah. You're right." Twilight then yawned and they both headed to the bedroom and began to sleep.

Charming Thunder was wandering through the halls of the castle which looked like the Crystal Empire. "There you are," a voice said from behind him.

"Huh?" Charming Thunder said as he turned to see his father.

“Your mother and I have been looking for you all over. It’s not becoming of a young prince like yourself to miss his lunch."

"Sorry," Charming Thunder said as he followed him into a large dining room.

"There he is," the cyan alicorn said as they sat down at the table. "Where did he go this time, Sombra?"

"He was wandering around in the castle again."

"Well he is defiantly an adventourous colt just like you, honey."

"And his magic. I saw him levitating ten books at once," Sombra said as a tray was placed on the table by one of the servants.

“Wow, ten books at such a young age,” the alicorn said impressed.

Charming?" a new voice asked as everything began to blur before completely dissolving.

"Charming Thunder, its time to get up," Twilight said shaking her husband with her hoof. Charming Thunder's eyes opened and looked around.

He then yawned then said, "Uh, what."

“You had another one of those dreams again didn’t you?” she asked looking at him.

“Yeah, but I have no idea what they mean," he replied stretching.

"Well I have a meeting with the princesses today. Why don’t you come with me and you can ask Celestia about it. You can bring the picture along to show her."

“Alright,” he said rolling out of bed to get ready for the day. He then rubbed his eyes and left the room with Twilight to start up breakfast.

Chapter 2: Berry Swirl

Charming and Twilight walked into the throne room of Cantorlot Castle and saw that only Celestia was present. “Good morning Twilight, Charming Thunder. What can I do for you to day?” Celestia asked.

"Well, I wanted to ask you about something," Charming Thunder said. "I’ve been having some strange dreams recently." He then levitated the picture out of his saddlebag and showed it to Celestia. "It relates to that cyan alicorn. I was just wondering if you know who she is."

“Hmm,” Celestia said looking it over. "I do know who she is. She is Princess Amidala. Wherever did you get this photo?"

"Princess Cadence gave it to him," Twilight said. "He also had a picture of his father with Star Swirl the Bearded."

"What else do you know about her?" Charming Thunder asked.

"Her name is all I remember. Not her past history." She then sighed and then said, "But the answers to all your questions lies with Star Swirl.”

“But he died hundreds of years ago.” Twilight said. “And his burial place has been lost. How are we supposed to find him?”

“At the far edge of the Everfree Forest lives an old hermit named Berry Swirl. He should be able to help you.”

“Alright, thanks," Charming Thunder said before they left the throne room.

“The day I’ve been dreading has come,” Celestia said once the doors had closed. “I can only hope that he can forgive me once he knows the truth."

The chariot that Twilight and Charming Thunder were on landed in front of a small house that was in the Everfree forest. “This is it.” Charming said as they got off the chariot and walked up to the small house.

“I hope Celestia’s right about him being able to help us.” Twilight said as they knocked on the door.

“Come in.” A voice said as the door was surrounded in a blue aurora before opening. Shrugging they walked into the small house.

“Berry Swirl?” Twilight asked as they walked into a living room like area.

“That’s me. How can I help you?” An old blue unicorn with a long white beard asked walking up to them.

"We have been told that you can help us," Charming Thunder said. "She claims that Star Swirl the Bearded can tell us about my mother." He then handed the photo to the old pony.

“Star Swirl the Bearded. Star Swirl…” Berry Swirl said thoughtfully as he looked at the photo. “Now that’s a name I’ve not heard in a long time. A long time.”

“Celestia said you would be able to help us find him. All the books say he’s dead.” Twilight said.

“Oh he’s not dead… Not yet.” The elder unicorn said after thinking for a moment.

"Do you know him?" Charming Thunder asked.

“But of course I know him.” Berry Swirl said with a laugh. “He’s me. I haven’t gone by the name of Star Swirl since… oh, before you were born.”

“But how?” Twilight asked confused as to how he was still alive.

“The princesses weren't the only ones to discover the secret to long levity.” He said with a wink. “I discovered a long levity spell during the Discord Wars.”

“Wait you fought in the Discord Wars?” Charming asked.

“Yes I was once a Crystal Knight the same as Sombra. Which reminds me, I have something here for you, Charming.” Star Swirl said as he walked over to a small box. “You’re father wanted you to have this when you were old enough, but Cadence wouldn't allow it. She feared you might follow old Star Swirl on some damn fool idealistic crusade like your father did.”

“What is it?” Charming Thunder asked as Star Swirl pulled out what looked like a crystal bracelet.

“It’s your father’s crystal saber. This is the weapon of a Crystal Knight.” The old unicorn said as Charming put it on and the crystal covered his hoof forming a blade. “Not as clumsy or random as magic, not to mention sharper than any regular blade; an elegant weapon designed for a more civilized age. For over a thousand generations, the Crystal Knights were the guardians of peace and justice in Equestria. Before the dark times… before the Republic.”

“How did my father become evil?” Charming asked as the crystal blade turned back into a bracelet.

“Your father was seduced by Discord into use of dark magic. When I first met him, your Father was already a great fighter, but I was amazed how strong his magic was. I took it upon myself to train him as a knight. I thought that I could instruct him just as well as Celestia. I was wrong.” Star Swirl explained sadly.

“I wish I had gotten to know him better.” Charming said sadly.

“He was the best sword fighter in Equestria. I hear you've become quite an accomplished fighter yourself. And he was a good friend.” He said cheering Charming up a bit. “Now what brings you hear?”

"We were told that you know who this cyan alicorn is. Is her name really Princess Amidala?"

"She is your mother." Charming Thunder's eyes went wide as Star Swirl asked, "Where did you find this picture anyway?"

"In the catacombs of the castle of the Crystal Empire. There were other boxes there and they are right now at my place. Do you know where my mother is now?"

"She's in the town of Manehattan. I told her that she would be safe there if King Sombra ever returned. Before she stayed there, she tried to turn Sombra back to the light, but when he saw me with Celestia and Luna, he became furious and almost killed her. I thought that I could redeem him as well but it was too late. The magic Discord made him become corrupted."

"And what of my fate?"

"When you were young, you were sent with Celestia and Luna to take care of you. But now that Discord returned and is now using his power for good, we are all safe."

"How will we find her, Charming Thunder?" Twilight asked. "The city is crowded." Charming Thunder then thought for a moment and then hatched an idea.

"I can request Celestia to send in some Prowler probes to scan the civilians to find her. If the ID of this picture matches, the droid can play a message from Celestia herself. She may know her more than I do."

"Why don't you come with us, Star Swirl," Twilight requested. "Everypony must know that you are still alive."

"No. That is not my destiny. I must remain here for now. When the time comes, I will reveal myself to everypony. I promise. Go now and tell your Celestia and Luna what you have learned today. If you ever want to know more about the Crystal Knights, you know who to look for. And remember, the magic will be with you always." Charming Thunder nodded and left the house of the legendary unicorn.

Chapter 3: Mystery of the Crystal Knights Begins

A 2.16 foot tall cyborg walked through the hallway of a battleship and entered the bridge. The cyborg wore a cape as he moved with his chicken-like feet. He also had cybernetic hands with six fingers on it. He also had a skeletal looking face of a non-pony skull with golden reptilian eyes. On his waist, he has a collection of lightsabers he made for himself. He coughed as he looked out of the window to view the town the ship is flying over. "Whats taking so long?" he growled and coughed. "We should be at Canterlot blowing the capital of Equestra to bits. I do not want to waste time just looking at a dumb city." The ponies who were at the controls started to get scared because of how intimidating he is. "I, Calamitous, cyborg general of the army, don't like waiting."

"Its going as fast as it could," the admiral said as he walked up to the tall cyborg. Calamitous then grabbed the admiral's throat and threw him across the room.

"I DON'T CARE!! I want to find this...Charming Thunder and make him suffer. I want to fulfill what Chrysalis could've done three months ago." He then growled at the grounded admiral as the troops cowered in fear. He then turned back to the window of the command bridge.

Charming Thunder placed his father's crystal blade in a glass case for display. The room was full of stuff that he brought home from the Crystal Empire. One mannequin displayed the armor of a guardian of the crystal knight. A brown robe barely covered the suit of armor. A knock was heard on the door and Rainbow along with Applejack entered the room. "Howdy," Applejack said.

"My friends," Charming Thunder greeted. "Its been far too long since the wedding." He then gave a hug to the duos as he asked, "How are things back at Ponyville?"

"Its going well," Rainbow said. "I just became a member of the Wonderbolt squadron and Spitfire is the leader of the squadron."

"Me and the apple family are doin' fine as well." Rainbow Dash then flew up to the portrait of Sombra wearing the Crystal Night armor with his crystal blade out. "Is this your father?"

"Eeyup."

"Wow. He looks awesome aside from being evil and all. Speaking of family, have you seen Twilight?"

"She's not here. She left to a meeting with the princesses about our discovery of the Crystal Nights."

"Crystal Knight? I only heard that they are a myth."

"Well, this bracelet here is the proof."

"The legend says that when you wear it, it transforms to a blade just like the one your father has," she said as she pointed to the portrait.

"I know. I witnessed it myself."

"Well we got to get going. It was nice seeing you again."

"Tell Twilight we said hi."

"I will," Charming Thunder said as Rainbow and Applejack left the room. He then looked back at the portrait and said to himself, "There are things you are not telling me, Aunt Celestia."

"Honey, I'm home," Twilight's voice said coming from downstairs. He then exited the room and walked downstairs to see her.

"Applejack and Rainbow were just here," Charming Thunder said as he walked downstairs. "They wanted me to tell you that they said hi."

"Oh, my best friends were just her. If only I were here sooner."

"Did you find anything important from my aunts?"

"As a matter of fact I did. Luna said something about an ancient temple. It is at the Crystal Empire so we probably should ask Cadence about it. And Celestia accepted the offer about finding your mother in Manehattan. She has already dispatched some troops and scanning droids to the town."

"Excellent. Once we find her, we will go to the temple."

The prowler scanning droid scanned roamed around the town of Manehattan to search for the target. The troops showed civilians a photo that was similar to the photograph that Charming Thunder had but only had the alicorns face on it. The pony nodded her head in disagreement and the troops moved on to the next group and asked the same question. A mare wearing a cloak over her head walked through the town. One of the droids noticed her and floated up to her face. "Scanning for target," the droid said. A ding was then heard and then said, "Target confirmed. Please wait for Equestrian troops to give you a message."

The mare removed her cloak and said to the droid, "I'm sure whoever you are looking for, I'm not the pony you're looking for."

Two armored soldiers walked up to her and one of them while they looked at the photo and back at her said, "This picture fits the details. May I ask for your name before we play our message from Celestia?"

"My name is Amidala." The trooper then took out his holo communicator and played the message.

"Princess Amidala, it has been so long ever since Sombra's defeat," Celestia said.

"Celestia, it has been a long time," Amidala said to herself.

"I wish to invite you to Canterlot castle to introduce you to somepony you may remember. My soldiers will help you take you to the castle." The message playback ended and the soldier holding the communicator puts it away.

"My...son. I hope that he's alright." She then followed the troops to the transport shuttle as she was about to go to Canterlot with them.

Chapter 4: A New Threat

Charming Thunder was at the Canterlot castle walking through the halls to the throne room. He entered the throne room with Twilight, Celestia, Cadence, and Luna present in the room. "Ah, Charming Thunder, you're just in time," Luna said.

"Why?" Charming Thunder asked.

"We have received word from one of the troops from Manehattan that they found your mother," Celestia announced.

"When will she be here?"

"The shuttle carrying her has docked at the hangar and is now heading to the throne room as we speak," Cadence said.

"I'm getting nervous about meeting her."

"Don't worry, Charming Thunder. We'll be here right beside you." A knock was heard at the door and Charming Thunder stood next to his wife as Luna said, "Enter." To doors opened and two soldiers entered. Behind them, a cyan alicorn entered and noticed the princesses.

"Guards, leave us," Celestia ordered. The soldiers then left the throne room and closed the door. "I'm so happy to see you, Princess Amidala."

"I am as well," Amidala replied. "It has been far too long ever since Sombra's first defeat. Is my son here? I want to see him."

"I'm right here, mother," Charming Thunder said. He then walked up to her slowly.

"Is it really you?"

"Yes. Do you not recognize your own son. I would never lie to my own mother." Amidala then ran up to him and gave him a hug and began to sob over his shoulder.

"Its been a long time, my son." They broke off the hug and Amidala kissed his forehead. "I heard that Sombra returned for the third time and you were the one who redeemed him from the dark side. Is it true? Is he really dead?"

"Yes, mom. He is dead. He sacrificed himself to save me from Chrysalis killing me." He then looked at his gloved hand as his mother placed her hoof on it. They both smiled and Charming Thunder sheds a tear and rolled down on his cheek. An explosion was heard from outside of the castle. Luna rushed to the window to see what was going on. She saw a battleship fighting through the Star Destroyer fleet and the ground forces are pushing through the streets of the town.

"Canterlot is under attack," Luna said.

"All of you stay here. I'll be back, mother."

"Be careful." Charming Thunder then ran outside of the castle and activated his lightsaber. The enemy soldiers wore black armor and a helmet. The troops aimed their weapons at him and started to fire at him. He blocked the shots back at them and took out the whole squad. As he moved on towards the town, he saw a six legged war droid that walked like a scorpion with blasters as its hands. It fired at Charming Thunder but he dodged the blasts and jumped over it. He then slice its head of and took out the rest of the ground troops that were heading towards the castle. At the distance of the castle gate, a Tsmeu-6 personal wheel bike was rolling his way with a cyborg driving it. It then jumped over him and its legs extended to land on the ground. He then jumped off of the controls of the bike and walked up to him.

"We meet at last, Charming Thunder," General Calamitous said. His cape flowed from the wind as it hanged on his back.

"Who are you and how do you know who I am?"

"I am Calamitous, general of the army and I have heard stories about you. You were the one who helped Twilight and her friends save Equestria dozens of times. I was a pony just like you. But one day when I was on a transport, a bomb that was planted on it blew me up. And now here I am. A cybernetic organism."

"So you were once a pony and now you're like this? But enough talk." Charming Thunder then activated his crimson blade and readied himself for combat.

"You fool." He flicked off a chain that was on his cape and grabbed two lightsabers. "You have no idea who you are dealing with." His cape fell to the ground and activated his blue and green lightsabers as he coughed. "Attack me if you dare." He started to twirl his cybernetic hands as he moved forward. Sparks flew as he twirled his blade on the ground. Charming Thunder was the first to strike but Calamitous used his left blade to block the attack. He then struck at his head but he blocked the strike with both of his blades and locked their blades together. Calamitous shoved Charming Thunder back then an explosion was heard. The Star Destroyers destroyed the battleship and the troops arrived and aimed their weapons at the cyborg general. He then chuckled as he got surrounded by Equestrian troops and said to Charming Thunder, "Army or not. You will soon realize that you are doomed."

"Try me," Charming Thunder said as he blasted Calamitous back with his magic. The cyborg then jumped over him and mounted his bike. He then rode through the squad and crushed them. he noticed that the gate is closed. He fired at the gate and rode out of the gate and escaped.

"Should we go after him?" the commander asked.

"No. Let him go. If we ever come across him again, we'll be ready." He then walked back to the castle to tell the princesses of a new threat he encountered and that is responsible for the attack as the troops returned to their posts.

Chapter 5: The Crystal Knight Temple

Charming Thunder entered the throne room and saw the princesses, his mother, Cadence, and Twilight are alright. His mother then walked up to him as she asked, "What was that all about?"

"We have a new enemy," Charming Thunder said. "General Calamitous."

"I've heard of that name," Luna said. "He was once a proud general before the wedding of Twilight Sparkle and Charming Thunder. He was an expert on tactics and a very good strategist."

"Interesting."

"Now that he has returned, he won't stop until you're dead, nephew."

"What must I do."

"For now you, Twilight, Rainbow, and Applejack will go with Cadence to the Crystal Empire to find whatever you can at the Crystal Knight temple," Celestia said. "If Calamitous ever shows his face again, we'll be ready."

I want to go too," Amidala said. "It has been a long time since I have been away from the Crystal Empire."

"Agreed," Twilight said.

"Not without me," a voice said from behind. Star Swirl the bearded stood behind them. The group were shocked.

"What are you doing here?" Charming Thunder asked.

"Its been a thousand years since I stepped foot inside the temple. I want to tag along."

"Its settled then," Cadence said. "We depart for the Crystal Empire immediately."

"I wish all of you the best of luck," Luna said.

"Even to you, Master Star Swirl," Celestia added. The group then exited to meet up with Applejack and Rainbow Dash as their quest was about to begin.

At the hangar, Rainbow Dash was readying the Eta-class shuttle as Applejack made sure that the fuel is in the ship. As the group arrived, she saw a bearded unicorn that she recognizes. "Are ya' Star Swirl?"

"Thats me."

"Oh my gosh. The world thought you were dead."

"Its a long story to be honest with you," Charming Thunder said. The group then walked up the ramp and saw Rainbow Dash pressing buttons to start the engines.

"Is the fuel loaded?" she asked Applejack.

"Yup."

"Alright. Crystal Empire here we come." The engines of the shuttle started to run as she flipped switches and pressed buttons. The shuttle then left the hangar and it plotted a course for the Crystal Empire.

The shuttle carrying Charming Thunder and the crew arrived at the Crystal Empire and landed at the docking bay near the castle. The ramp of the shuttle then lowered and the group walked out. As they left the docking bay, they came across the temple of the Crystal Knights. The stairway lead them to the entrance to the temple. As they entered the temple, Applejack turned on a flashlight on her helmet and revealed a hallway with collapsed and barely destroyed statues of the Crystal Knights. "So this is the temple?" Charming Thunder asked.

"It is," Twilight said. "But...what happened here?"

"This happened when Sombra betrayed us. He came alone and slaughtered everypony in this temple." The group then continued on through the hallway to find a power switch and turn on the lights. They entered the power room and flipped the switch. The lights then turned on in the whole building. "There is a library if you are interested in looking around.. There we store information about the fallen knights and the history of the famous heroic knights."

"Twilight and I will check it out," Charming Thunder said.

"Rainbow and I will check if the elevators are working," Applejack said.

"Me and the princesses will take the stairs to the second floor to look around," Star Swirl said. The group then broke off as Charming Thunder and Twilight entered the library. The library had huge shelves full of books that barely got destroyed. Twilight flew up to one of the shelves to start reading one of them as her husband saw a door in the back of the room. He walked up to the door and slowly opened it. Birds then flew out of the door which startled him in the process.

"You alright, honey?" Twilight asked.

"Yeah. I'm alright. It was just birds." He then entered the room and came across a blue glowing cube shaped object. "Hey, honey. I think I found something." Twilight then flew in the room where Charming Thunder was and saw the object he levitated up. A few seconds later, a hatch where he got it from slowly opened. It revealed a red and gray metal mask.

"What is it?" Twilight asked.

"Its...a mask. Whats it doing in here. I don't know what this cube thingy is but I think we should show it to Star Swirl.

"Great idea. I'll grab a couple of books to bring home so that I can read them." She then left the toom and collected as many books as she could. Once she finished, she met up with Charming Thunder and decided to explore more.

Applejack and Rainbow Dash arrived at the area where the elevators are and pressed the button to lower it down. The elevator doors then opened and they entered. The elevator then went up as they waited for it to stop at the floor it was designated to go. "So, AJ," Rainbow said. "What else do you know about these Crystal Knights?"

"I also heard that in this temple, there are spirits of the dead around here," Applejack explained. "Like Star Swirl said, Sombra was the one that destroyed every pony in this building."

"Ghosts? Ha!"

"But thats not all, some say that at the top of the tower were heading to is the place where the spirits of the council lurk."

"Again with the ghost stuff."

"i'm just joking' with ya'. There are no ghosts in here."

"You had me worried there." The elevator beefed and the door opened to reveal a room that has chairs formed in a circle at the windows.

"This must be where the council was seated. And look at these chairs."

"Yeah I know. These chairs are still in great shape. Even if we sit on them." Rainbow then sat on one of the chairs as she looked around.

"The view does look great up here. Look. I can see our ship from here." Rainbow and Applejack looked out of the window and saw ships flying out of their docking bays and landing pads. "It makes me like a ruler of this kingdom."

Chapter 6: The Holocron of Regal Crescent

Star Swirl, Cadence, and Amidala were exploring the second floor and entered a room which had a beautiful view of the kingdom. "This room use to be a place where we practice their skills with a weapon," Star Swirl said. Cadence then opened a door to reveal some fighting dummies that is now covered with cob webs and dust. They all then noticed Charming Thunder and Twilight heading their way. They exited the room to find out what they saw at the library.

"What did you find?" Cadence asked.

"We just found a couple of books," Charming Thunder said. "And this cube looking thing along with this mask." He then took out the cube and the mask out of his saddlebag and showed it to them.

"Oh my," Amidala said. "Thats a Crystal Knight data holocron. Its an an organic crystal-lattice device which stored phenomenal quantities of data. It contains data from knights from a thousand years ago."

"How do you access it, mother?"

"It requires a lot of concentration and focus. Once opened, you will be guided by the one who made this holocron."

"Why don't you give it a shot," Twilight said.

"Okay." Charming Thunder than sat down and his horn glowed as the holocron glowed blue. He then opened his eyes and noticed a small unicorn figure wearing a robe and the same mask he found with his horn popping out.

"I am Regal Crescent, member of the Crystal Knight order." he said. "I was the greatest war hero Equestria ever knew. I once possessed dark magic before Sombra did. Once I was corrupted by dark magic, I was redeemed by Princess Celestia and Princess Luna. In the end, I thought I was lost to darkness. When Sombra joined the order, he became obsessed with learning about dark magic, but the council forbid him. When Discord betrayed the princesses, he gave him dark power he could ever imagine. It then made him become king of the Crystal Empire and he marched to the temple and wiped out all of the Crystal Knights. And in the end, the temple was now and forever destroyed. If Discord ever returned to the good side, he could never be trusted and he would soon destroy us all. The council knew hat one day somepony will rise up and put an end to the dark king." The figure then faded away and the holocron stopped glowing.

"I guess that explains why the temple is like this," Cadence said.

"Come on," Charming Thunder said. "Lets check out the top floor. That is where Applejack and Rainbow Dash are right now." The group then nodded in agreement and entered the elevator.

General Calamitous was seated in his chair on the Interdictor-class cruiser as he plans an evil pot to overthrow the Equestrian Empire. An admiral entered the room to speak to him. "We have received reports that Charming Thunder is at the Crystal Empire," he said. "He and his friends are exploring some sort of temple."

The general stood up from his seat as he said, "Plot a course for that temple. I have plans for our unicorn friend."

"Yes, sir." The admiral then left as Calamitous looked out of his window.

The elevator the group was standing in beeped as the doors open to reveal the council chamber. Rainbow Dash and Applejack were sitting on one of the chairs that are in the room until they noticed them. "Hey, guys," Rainbow said. "Care to try out these chairs?"

"These chairs belonged to the council of the masters," Star Swirl said as the group took a seat. Cadence looked out of the window and saw her kingdom in a gorgeous view.

"So this room belonged to the council of the masters, huh?" Charming Thunder said. "Tell me more about this Regal Crescent."

"He was a great war hero. He was the one who ended the Griffon war and brought peace to the griffons and ponies. But on that fateful day, he returned somehow corrupted. He was then redeemed with the help of the princesses.That mask he found once belonged to a griffon leader he killed."

"So this mask is a symbol of his legend?" He then looked at the mask that he found in the library. "He said that he knew my father. Is that true."

"Yes. As a matter of fact, Regal was a good friend to him. Your father learned much from him. From magic to sword fighting. I was amazed myself that my student learned well from a famous war hero."

"Tell me about the masters."

"They are the members of the council. I am one them for unicorns along with the pegasus Firefly, the earth pony Strong Shield, the minotaur Iron Steal, the griffin Hilda, the horse Jibril, the diamond dog Rex, and the drake Draco. This temple was founded by me, Apple Seed, and Lightning Dash in order to maintain peace between the three pony tribes when Celestia and Luna first came to power. The first of the Knights where trained by Princess Celestia and Luna. They would then pass down what they learned onto the next generation."

"Lightning Dash? Thats one of my ancestors," Rainbow said. "I didn't know that he was a Crystal Knight."

"You are correct. Firefly was the one who found the Wonderbolts and Strong Shield was one of the first leaders of the royal guard. Since Sombra took over the Crystal Empire, the remaining Crystal Knights went out into hiding. They were then fully disbanded when the first Lunar Republic was founded by Nightmare Moon."

"Was there a zebra in the order?" Cadence asked.

"Yes there was. She was a member of the council as well. But I can't remember her name."

"Um. I hate to interrupt but we got company," Applejack said as she pointed to the window. The group then saw a cruiser flying this way. In the distance, an assault shuttle was heading their way.

"I think we should start running," Amidala said.

"I'll stay," Charming Thunder said.

"No you are not. You are coming with us."

"Calamitous is only here for me. Go to the shuttle and meet me back at Ponyville. I'll handle that reptile eyed cyborg." Twilight walked up to him and pressed her lips to his.

"For luck," Twilight said. The group then ran off to the elevator and went down to the main floor to escape. Once the others escaped, Charming Thunder waited for Calamitous to come face him alone. When the shuttle touched down to the ground, the ramp on the side opened and the door opened to reveal Calamitous. He walked down the ramp and entered the temple to start his search for Charming Thunder. "I know you are here, Charming Thunder," Calamitous said as he walked through the hall. The shuttle that Raibow Dash and the group were in left the docking bay and flew to the direction to Canterlot so that they can alert Celestia about what they discovered.

Chapter 7: The Great General Falls

The shuttle landed in the hangar and the ramp lowered. Twilight an the others rushed to the throne room to a let Princess Celestia and Princess Luna about the situation Charming Thunder is in. They entered the throne room and stopped to catch a breath. "What's going on?" Celestia asked.

"Where's Charming Thunder?" Luna asked.

"Calamitous just arrived at the temple unexpected," Twilight said. "We came here to tell you that and request that we send a squad over to the Crystal Empire to help him."

"If he needs our help, then we must send our forces right away." Luna then turned to a guard. "Alert the forces and tell them to head to the Crystal Empire. And ready Celestia's armor and mine."

"Right away, your highness," the red guard said. He then rushed out of the throne room to do the task that was given.

Charming Thunder stood on the ledge on the second floor as Calamitous searched for him. He then leapt down behind him and said, "Hello there." The cyborg general then turned to see him.

"Charming Thunder," Calamitous said as he chuckled. "You are a brave one. I am here to settle the score for real this time."

"Your move." Charming Thunder then ignited his crimson blade and readied for combat.

"It will be your funeral, puny unicorn." He then reached for four lightsabers and splits his arms as he activated his blades. He then jumped to strike at Charming Thunder but he blocked the strike. Charming Thunder then made some strikes and chopped of one of Calamitous' hands. The cyborg then looked at his chopped off hand and used his fury to strike his opponent. During a clash, Charming Thunder lowered his lightsaber to chop off the general's other hand. They once again entered a clash and Charming Thunder gritted his teeth. Calamitous then pushed him back until they heard an explosion sound. The Equestrian troops came out of nowhere and started firing at Calamitous' army. "Army or not. You will soon fail in the end."

"Oh, I don't think so." Charming Thunder fired magic which caused Calamitous to drop his lightsabers and hit a wall. He then pressed a button on his cybernetic arm and his wheel bike rode in. He then manned the bike and began to ride off. Charming Thunder ran after him and jumped on the back of his seat. The general then piloted the bike up a house which caused Charming Thunder to drop his lightsaber. Applejack was firing at some enemies when a lightsaber hit the ground next to her. She picked it up and looked at the direction where it came from.

On the bridge of the Star Destroyer, Celestia, Luna, Cadence, and Twilight watched as the battle raged on in the air when a hologram of Applejack came. "Princesses," Applejack said. "We have landed and encountered enemy resistance. We have begun our attack."

"Very well, Applejack," Celestia said.

"Continue as planned," Twilight said. "We'll be down as soon as we could." The transmission then ended as the princesses left the bridge and headed to the hangar to join the forces on the ground.

The wheel bike jumped and started to climb on the castle. Charming Thunder hung on and jumped behind the general. As they reached the top, Calamitous reached for his electro staff and tried to hit him. Charming Thunder then dodged and grabbed the staff out of his hands. He then tried to hit the general but he kept on dodging. As Charming Thunder has the staff between the cyborgs neck, Calamitous grabbed his blaster and tried to shoot him. The shot then made them fall off of the wheel bike and landed on the top of the castle. Charming Thunder grabbed the staff and rushed to attack him. The general fired and the staff hit his hand which made him drop his blaster. Charming Thunder then hits his chest and made him collapse to the ground. The electricity on the staff then impacted on the downed cyborg and the general kicked him away. He then got up and tried to stomp on the fallen unicorn. He then grabbed his neck and lifted him off the ground. Charming Thunder used his magic to open up his chest and saw the generals heart beating. The cyborg then hits him in the face and he rolled away. As Calamitous got his clawed foot stuck, Charming Thunder kicked his leg but got hurt in the process. Calamitous then picked him up and threw him to the edge of the castle. He then picked up the staff and walked up to the unicorn as he was hanging on for his life. Charming Thunder used his magic to get the blaster and grabbed it. He aimed the blaster to his chest and fired. The cyborg growled after the first shot. He then fired again and again until the general exploded and fell to the ground. Charming Thunder then climbed up and walked up to the fallen general as he threw the blaster aside and said, "So uncivilized." He then heard the battle going on down below and teleported to the door in the castle. He heard explosions outside the castle as he opened the door. The battle in the streets raged on as he started to run through to find Applejack. He then saw Applejack and rushed to her side. "Applejack, contact your troops and tell them to move to the roof tops."

"Great idea," Applejack said. "Oh, by the way." She then grabbed the lightsaber off of her belt and gave it to Charming Thunder. "I think that ya' dropped this."

"Thank you. Now lets move. Enemy reinforcements are coming and we have a battle to end here."

"Yes, sir." Applejack and the squad rushed to the rooftops of the houses as they setup a trap for the enemy.

Chapter 8: Springing the Trap

Applejack, Charming Thunder, and the squad are on the rooftops as they wait for the enemy to come. Applejack took a peak through the binoculars as she hid to see what they are up against. She saw five war droids, five cloaked ponies wearing a mask, and a gray unicorn in front of the army. The unicorn wore an armor with shoulder pads an a cape over his armor. He had yellow reptile looking eyes as he looked forward. The rest of the forces she saw were just infantry. She then got back to cover and reported, "They're getting close."

"We must hold here until the princesses arrive," Charming Thunder said to the soldiers. "We will fight. To victory." He then raised his blaster as he yelled, "FOR THE EMPIRE!!!" He then fired his blaster at one of the soldiers and used the grenade launcher on his rifle to destroy the war droids. The soldiers then jumped off of the roof and began to fire at the enemy forces. The gray unicorn activated his crimson blade and used his magic to levitate a soldier up and pull him straight to his blade. He then looked at Charming Thunder as he walked to him. Charming Thunder noticed him coming and launched three grenades at him. The unicorn deflected two but one managed to blow up and scaring the gray unicorns muzzle. Charming Thunder then dropped his weapon and charged at him. The unicorn then assaulted him with lightning. Charming Thunder barely resisted it until the lightning pushed him across the battlefield.

A few seconds later, Charming Thunder opened his eyes to see his army being crushed by masked figures with their lightsabers. He turned to see the gray unicorn finishing off a soldier. He then turned to Charming Thunder and smiled at him. A masked pony then walked in front of him and activated his lightsaber. When the pony was about to kill him, a blast of magic came out of nowhere and killed the masked pony. The soldiers that were holding Charming thunder also got blasted to the chest and released him. The unicorn then turned to see Celestia, Luna, Cadence, and Twilight landing in front of Charming Thunder.They both then grabbed their lightsabers and activated them. Charming Thunder got up as a soldier gave him a rifle an the four alicorns began to fight the remaining masked ponies and the gray unicorn himself. Charming Thunder fired at the enemy troops as the duel began. Celestia, Luna, and Cadence already struck down their opponent as Twilight faced the unicorn. The unicorn then pushed Twilight to the wall and Charming Thunder noticed her about to be defeated. He then rushed to the unicorn as he yelled to get his attention and tackled him to the ground. He punched him in the face and did a head-butt on him. He then placed a detonator on him and got out of the way. The explosion impacted him as he ran away and knocked him out to the ground. Celestia, Luna, and Cadence then landed in front of the scarred unicorn and blasted him to the wall. As the unicorn struggled from the blast, the final blast from Celestia destroyed the building the unicorn was blasted on and the rubble landed on him.

A few minutes later since the battle ended, Charming Thunder came out of unconsciousness and looked up to see the damage the battle did to the Crystal Empire. He then saw Twilight run up to him and gave him a tight hug. "What happened?" Charming Thunder asked.

"The battle has ended," Twilight said. "We won."

"We...won?"

"Yes, honey."

"What happened wit that unicorn?"

"He was dragged out of the rubble by his troops and retreated far away from this kingdom," Luna said as she walked up to him. "At least the general is dead."

"Yes. And now we have a new enemy. I don't know who they are, but they will pay for what they did to the Crystal Empire."

"I'm sure that the crystal ponies would be very grateful for your service here," Applejack said. "First Spike and now you."

At Canterlot, a parade was going on outside of the castle as Charming Thunder and his wife watched with the princesses and his mother. "We have gathered here to honor a unicorn who saved Equestria once again from an unknown enemy that attacked the Crystal Empire," Celestia announced to the audience. Luna then levitated a medal with a symbol of the Equestrian Empire and placed it around his neck.

"We present you this medal of honor," Luna said. "Keep it as a symbol of a new hope for Equestria. Wherever the enemy strikes we will be ready."

"Thank you, Aunt Luna and Aunt Celestia," Charming Thunder said as he walked up to them and gave them a hug. Twilight and her friends watched as the audience cheered. He then walked up to Twilight and kissed her on the cheek.

The battle damaged unicorn now wore a cybernetic respirator as he laid in the bed. "Our forces have made it past the enemy fleet and are arriving shortly," the officer said.

"Good," the unicorn said. "Inform the troops that we will strike when the time is right."

"As you wish, Lord Malgus." The officer then bowed and left the room as Malgus now plans to have his revenge.

Charming Thunder sat on a couch with Twilight cuddling together. "Charming," Twilight said.

"Yes?" Charming Thunder replied.

"What did you do with those artifacts you found at the temple?"

"Oh, I just put it in the room where my father's stuff is stored. The holocron is safe where it belongs." The holocron in the room was displayed in a glass case on a pillow next to the crystal knight bracelet. It then started to glow like a firefly as it sat in the case.

THE END

Prologue

Once upon a time in a magical land of Equestria....

EQUESTRIA WARS

Episode IV
Shadows of Equestria

It is a time of peace and justice in Equestria. The Lunar Republic is gone with the Death Star destroyed once again and the birth of the Equestrian Empire.

Three months later since the war ended, Twilight and Charming Thunder have finally moved in together in Canterlot and got married.

Charming Thunder now sets out to the Crystal Empire to visit his sister to seek more information on his father’s past and find out who his mother is....