The Changeling Civil War

by ShadowGear

Rating: teen
Tags: My Little Pony: Friendship is Magic, Dark, Alternate Universe, Sad, Main 6, Romance, Changelings, Original Character, Cutie Mark Crusaders, Queen Chrysalis, Adventure, Tragedy
Length: 4646

Thorax had become the new king of the Changelings and the other Hives are not happy about his alliance with Equestria. Will Equestria survive against the upcoming Changeling invasion? How will they fight against a technologically advanced enemy?

Thorax had become the new king of the Changelings when they joined Equestria. Queen Chrysalis had sworn revenge and was forced into exile. She is now gathering her allies from the other Hives in an attempt to retake her throne and finally end the conflict with a victory for the Changelings. One Changeling named Sclerite, was not around when Thorax came to power and would play a major role in the upcoming war.

This is an alternate story to "Hidden in Plain Sight" You don't have to read the previous stories to understand this one.

Published 2017-08-03 13:00:12 UTC
Last updated 2017-08-17 22:05:23 UTC

Prologue: The Alliance Mobilizes

Sclerite stood on a small island in the middle of the ocean. He could hear the sounds of waves crashing against the shoreline, but that didn't matter to him. He was waiting for the others to arrive. Ever since more and more ponies began to brave the Everfree forest, the Allied Hives had abandoned The Castle of the Two Sisters, the secluded island became their neutral ground to hold secret meetings.

Suddenly he heard a loud crash and looked to see five large, almost rectangular ships emerge from underwater. A hatch opened at the top of the lead ship and a Changeling with purple eyes and a purple chitin climbed out. She wore an officer's helmet.

Sclerite immediately saluted, "Admiral Seta! Welcome! I've already prepared the meeting table for the Queens." He had known about Admiral Seta mostly from gossip. She had led many hit and run wolf pack tactics against Equestrian trading ships. Many have nicknamed her, "The Kraken," because of the amount of terror she had caused in Equestrian costal cities such as Manehattan.

Admiral Seta flew out of the U-ship and landed in front of Sclerite. "Lieutenant Sclerite, I want to say, 'congratulations,' your training is finally over. You are now an official soldier of Queen Chrysalis' Hive. In fact, Queen Chrysalis had personally requested for you to come here with the other Queens," she said.

Sclerite looked surprised. After being given around to many Queens, he thought he had been forgotten. "Do you have any idea when Chrysalis and the other Queens will arrive?" Sclerite asked.

"The Queens Siphon and Formic came with me. I'm not sure when Queen Chrysalis would arrive," Seta answered.

"Well then, I guess we'll just have to wait," Sclerite said.

Queen Siphon and Queen Formic left one of the U-ships and Queen Siphon ordered Admiral Seta to form a blockade until they leave. The U-ships dived back underwater. It wasn't long until the other Queens came. Some had Changeling bodyguards with them. Eventually, Chrysalis arrived and landed in front of Sclerite. He bowed respectfully as she looked down at him.

"Sclerite! My apprentice! It's been a while since I've seen you!" she said.

Sclerite looked up. "My Queen, it is an honor to see you again!" he said.

"That's great, I have need of your services one again, but first! I want you to attend this meeting with the other Queens as an observer!" she said.

Being able to even witness one of these meetings was an honor. Although he was Chrysalis' apprentice, he didn't believe he would ever have the privilege. "Thank you my Queen! You're generosity knows no bounds," he said.

Queen Chrysalis and Sclerite approached the table Sclerite had set up hours ago. On it was a map of Equestria and a bit of Griffon territory on the other side of the ocean.

Queen Chrysalis did a quick headcount before speaking. "You may be wondering why I called you all here. Well a terrible thing has happened to my Hive! They have succumb to the corruption that is Equestrian friendship! They have no idea that it is a trap and the Equestrians are planning to betray them, and slaughter them to the last! I am in desperate need of the Alliance if I'm ever going to save my drones from such a terrible fate!" she said.

The table was filled with whispers until Queen Formic stood up. "Listen! We agreed to join forces to face the Equestrian threat as one! It is time we show the Equestrian princesses that we wont submit to them without a fight!"

Queen Siphon stood up as well, "The Equestrians have gone too far this time! We've let them conquer the Dynasty of Mules, as well as destroying the old Draconequus kingdom. The destruction of an entire Hive is the last straw! I say we declare open warfare against Equestria!"

The other Queens began to chant, "Stop Equestria!"

Suddenly Chrysalis shot a beam of magic into the sky to silence everyone. "If we are going to attack Equestria, the first order of business is to reconquer my old Hive. I volunteer Sclerite to lead this attack," she said.

The Queens began to speak amongst each other once again to decide on what to do. Eventually it was decided and Queen Formic summarized the plan. "My Hive will provide Sclerite a platoon of tanks. He will also be given an entire battalion of Changeling soldiers comprised of multiple Hives. While this is going on, Admiral Seta and General Tarsal will plan out our initial invasion against Equestria. Sclerite will receive his next orders once he has retaken the Hive."

"Alright, Sclerite. You have your orders. I trust you wont disappoint me," Queen Chrysalis said.

"Don't worry my Queen, I'll take back the Hive and save those drones," Sclerite responded. This was sure to be his moment of glory. The day he would prove his worth to Queen Chrysalis.

"One more thing. The Changelings support Equestria now and would actively resist your attempts to retake the Hive. You will have to fight them like they were enemy combatants," Queen Chrysalis said. "I suggest you prepare yourself for the battle ahead."

Sclerite stood up and noticed the U-ships had returned. It was time for him to leave and he couldn't just swim or fly all the way back to the mainland. Sclerite boarded a U-ship and it submerged.

Author's Note

I'm back after a long break from fimfiction. I would really like to know what you all think of this story. Don't be shy I really need the advice since I've never really written a war story before.

Chapter 1: Operation Liberation

Sclerite stood in front of a familiar place. It was where he had seen that massive rainbow explosion in the sky. Nopony other than him knew of this place until now. Now this was where Sclerite would siege the Hive that once kept him safe. his troops were assembled. There were about ten tanks with at least thousand troops comprised of members from multiple Hives. That wasn't the only thing they had in their arsenal. There was also anti-air guns and artillery made of the same magic siphoning minerals used on most of the Allied Hive's weaponry.

A Changeling approached Sclerite, "Sir, our forces are assembled and we are awaiting your orders."

"Very good, keep our tanks in the front. I'm going to join the army as we advance," Sclerite said.

"Sir, yes sir!" the Changeling said before rejoining the army.

Sclerite waited until the tanks began to move. They had formed a straight line and were going to cross the barren land where there was no cover. Apparently the enemy noticed this and flew down to meet them. Sclerite quickly ran to the front just in time to greet the welcoming party. He had not expected to see this. There was a large, green bug that had two large antlers, as well as diamonds on his chest.

Sclerite wasn't sure what to say. He was not prepared for anything like this. The strange bug noticed Sclerite and was visibly frightened. "Sclerite? Is... Is that you?" he asked.

Sclerite swallowed whatever nervousness he had and spoke, "I have come to take the Changelings back into Queen Chrysalis' Hive."

The other Changeling began to calm down. "We are independent now! Chrysalis was going to lead our Hive to ruin!"

"Siding with the Equestrians will lead the Changelings to ruin. Besides, how are you going to ensure the survival of your new kingdom after this generation. It's not like you have a Queen," Sclerite said. "I'm here to save you from the Equestrians. If you don't cooperate and allow us to take back what's ours peacefully, I will have no choice but to do it by force," Sclerite threatened.

"I will not let you destroy our freedom!" the Changeling said before quickly flying off.

"As you wish, all troops prepare to attack the Hive!" Sclerite yelled out.

The tanks began to fire magical bolts of energy into the Hive. Pieces were falling off but the Hive itself rapidly regenerated the broken structures. The rebel Changelings responded immediately by flying towards the group. They were planning to dive bomb Sclerite's army.

"AA guns! Take them down!" Sclerite ordered.

Suddenly the forest was lit up with green magical bolts as they flew through the air and exploded. The rebel Changelings were quickly torn apart by the flak. It was a horrible sight, most of the rebels lost large sections of their bodies and even entire limbs. The survivors were screaming in agony. The sight made Sclerite sick but he pretended it didn't bother him.

"Surrender now! There is no need for anymore bloodshed today!" Sclerite called out, using magic to amplify the volume of his voice.

A few minutes later, there was a large white flag planted at the top of the Hive. However, Sclerite was able to see one of the rebel Changelings flying away. It didn't matter though, he had won without suffering any casualties on his side. Hopefully this would be the first of many victories.

Chapter 2: The Warning

Flurry Heart giggled as Cadence played peekaboo with her. Shining Armor stood at the door, smiling at the sight of his wife and daughter. Trying the perfect balance between raising Flurry Heart and ruling the Crystal Empire was not an easy task, but they've managed.

Suddenly Thorax flew in through the window and crashed onto the floor. He looked as if he had flown nonstop for miles.

Cadence and Shining Armor stopped what they were doing and rushed over to help Thorax. "What's going on?" Cadence asked.

Thorax was dizzy from the crash but his head was still clear enough to respond. "Queen Chrysalis is back, and she has an army by her side. They just retook the Hive. I came here as fast as I could to warn you," Thorax explained.

Shining Armor made his way to the door, "don't worry Thorax. I will lead an army and liberate your people-"

"No! They have weapons we've never seen before!" Thorax interrupted.

Shining Armor stopped at the door. "What do you mean?" he asked.

"We had the enemy hopelessly outnumbered but they unleashed some kind of secret weapon against us. It destroyed us before we could get close enough to fight back. I ordered my people to surrender and came here by myself to warn you about this new threat," Thorax explained.

Shining Armor and Cadence remained silent. The only sound in the room was Flurry Heart flying around and giggling. Eventually Cadence broke the silence. "We should get a letter to Canterlot as soon as possible," Cadence said.

"I'll write the letter," said Shining Armor as he rushed out the door.

Meanwhile at the Changeling Hive. Sclerite had successfully defeated the rebel Changelings, and had recently finished setting up four tiny scarabs on a rock outside of the Hive. A large image appeared with each of the Queens.

"My Queen, we have taken back the Hive and are awaiting new orders!" Sclerite said.

"Very good, prepare to head north to the Crystal Empire," Queen Chrysalis ordered.

"It shall be as you say my Queen," Sclerite responded before he cut transmission. He immediately turned around to see one of the rebel Changelings approaching him. The Changeling was stopped by two red Changelings from Queen Formic's Hive.

"Sclerite, why are you still loyal to her?" he asked. Sclerite immediately recognized who it was.

"Carapace, let me ask you one question. Did you really think the Equestrians care about Changelings? Don't you remember the history lessons? They are conquerors, many great civilizations once stood at these lands. All of them were destroyed by Equestria or turned into puppets. I will not let the same thing happen to you nor any other Changeling," Sclerite said. "I'll be leaving pretty soon. What I want to know is, why did you betray us?"

"Thorax had shown that we don't need to steal love. We can instead share it among each other," Carapace answered.

"You know, I really wish that was how it was before I had left to train with the other Hives. I always wished I could have been like you guys. That would've saved me from the insults you all threw at me, but now I'm glad I was singled out. At least I can remain pure," Sclerite said before leaving to check up on his troops. "I want this tank column ready to move! We are heading to the Crystal Empire!" Sclerite yelled.

The tanks roared as they began to move. A total of five hundred Changelings accompanied them as they left half of the anti-air guns in the once secret area.

Chapter 3: The Siege of the Crystal Empire

Sclerite assembled his forces outside the Crystal Empire. There was a large shield surrounding the city. Sclerite recognized it during the attack on Canterlot. It was made using the undeniable power of love between two ponies and was the sole reason why they lost the battle. However the shield was the last thing on his mind. They had been trekking through the harsh terrain for almost an entire day. Everypony was exhausted and the tanks couldn't provide enough heat for everyone. Morale was extremely low and Sclerite could hear his troops whispering about deserting while his back was turned. Sclerite himself almost lost any hope of reaching their destination. The sight of the empire almost made him jump with joy.

"We are setting up camp!" Sclerite ordered. "Position the tanks in front and the artillery right behind them. Keep me informed about any moves the Equestrians might make."

"Sir! There is a cave over here!" yelled out one of Sclerite's soldiers.

"Very good! I need volunteers from Queen Formic's Hive and Queen Enzyme's Hive to keep watch while everypony else rests!" Sclerite yelled out.

Many hooves flew into the air and it was hard to decide who to choose. Eventually after picking randomly, the Changelings dispersed to gather wood and set up fires inside the cave. Sclerite stayed outside with the volunteers to set an example to his soldiers.

Meanwhile at the Crystal Empire. The Crystal pony guards were on full alert when their scouts spotted the large Changeling army. Shining Armor had set up the magical shield, hoping it would slow the enemy down.

"Flash Sentry! Front and center!" Shining Armor called out.

A young Pegasus dressed in Canterlot Royal Guard armor rushed over to the prince. "Yes sir?" he said attentively.

"I am placing you in command of the Crystal Pony guards. I want you to destroy or weaken the enemy before they can breach my shield," Shining Armor ordered.

"Yes sir!" Flash Sentry said before running off.

Thorax approached Shining Armor. "I think you should reconsider your attack. It might be better if we evacuate everypony we can," Thorax advised.

"Don't worry. I've been a captain of the Canterlot Royal Guard for a long time. I wouldn't send my stallions into battle without even a remote chance of victory," Shining Armor assured.

Thorax looked at Flash Sentry. He was busy directing the soldiers and forming battle lines. "I can't watch," Thorax said to himself before flying off to the Crystal Palace.

Sclerite stood vigilant with his Changeling forces. While they were taking shifts with the other troops, Sclerite had refused to leave. He began to feel drowsy and was on the verge of closing his eyes when he heard a tap coming from one of his sentries.

"Sir! The Equestrians are getting into formation, and are headed this way! ETA till contact is thirty minutes!" the red Changeling said.

Sclerite snapped back into reality. "Prepare the artillery!" he ordered.

The Changelings currently on look out began to aim the artillery at the approaching enemy army. The tanks roared to life and turned their cannons towards the Equestrians. "Sir, artillery is ready!" said a purple Changeling.

Sclerite cleared his throat, "fire!"

Author's Note

Check out my blog to vote for the what happens next.

Chapter 5: Frag Attempt

The Green Changeling named Spiracle dragged Sclerite into the cave. Most of the Changelings were still asleep but many noticed Sclerite. Some came to help her while others stared or whispered amongst each other.

"There you go sir," Spiracle said to Sclerite as she positioned him near a fire. She could hear him breathing normally. The room was full of whispers.

"Is that the Lieutenant?" asked one of the nearby Changelings.

"Yeah, this is our chance. It's now or never," whispered another.

Spiracle noticed a few Changeling soldiers standing up from the nearby fires. Some of them continued to watch while three Changelings slowly approached.

"Can I help you?" Spiracle asked to he nearest one. She took up a defensive posture like a bear protecting a cub.

"Medic, we have to do this. Sclerite led us into a frozen grave. He has to go," explained one of the Changelings.

"No! He is our commander! I'm not going to let you hurt a defenseless soldier!" Spiracle yelled. Many Changelings woke up from the noise.

"I'm sorry," he said right before he swung a hoof at her.

Spiracle immediately charged him before the hoof could connect and shoved him back with the force of her movement, causing him to fall over. She may be a medic but she had been trained for self defense. These soldiers had made the mistake of underestimating her. The other Changelings realized what was going on and charged into the brawl. One of the Changelings quickly held out a small red horn and tried to stab Sclerite with it but was stopped by Spiracle who used his momentum to knock him to the ground. The other Changelings tackled the rest while Spiracle kept the one with the weapon on the ground. She held his hoof with the weapon in a really uncomfortable angle which kept him from attempting to stand back up.

Sclerite suddenly shook his head and opened his eyes only to see three Changelings being held down with one of them having a strange horn. It was red and was curved shape. The horn could've been part of a unicorn at one point but he had never heard of any unicorns with horns like that.

"Sir! Are you alright?" Spiracle asked when she noticed Sclerite's open eyes.

"Yes, I'm fine. What happened?" Sclerite asked, looking around at the Changelings that were pinned to the ground.

"You had fallen unconscious outside. I had to drag you back into the cave. That was when these Changelings attempted a mutiny," Spiracle explained.

"Thank you, what's your name?" Sclerite asked.

"I am Sergeant Spiracle," Spiracle answered.

Sclerite stood back up. He was still incredibly tired but his rest could wait until this situation was dealt with. The Changelings dragged the attackers and lined them up. He noticed something when he stared at their eyes. A purple aura made of dark magic was spilling out.

Sclerite grabbed the horn. "Where did you get this?" he asked.

"It was deeper in the cave," one of the attackers fearfully answered.

Sclerite had never seen magic like this. It seemed like mind control magic to him. "Place them under arrest. I need to look into this before I make a decision," Sclerite ordered. "And Spiracle, thank you."

"You're welcome, sir!" Spiracle responded while feeding off of his appreciation.

Sclerite dug a small hole with his hoof and buried the horn underground. He then used his magic to draw an X at the spot before going back to sleep.

Author's Note

I want to say sorry about what I said to you guys last chapter. It wasn't right for me to lash out at my readers because I was angry. I don't expect any forgiveness but I'm not going to leave it unsaid. If you accept my apology, I would like to know. Otherwise, I deserve anything you have to say to me.

I wonder if I am socially abusive.

Chapter 6: The Fall of the Crystal Empire

"Sir!" called out one of the Changelings. The sudden call woke Sclerite who immediately stood up. He looked around and noticed that it was Spiracle who had awoken him. "The Equestrians are calling for reinforcements!"

"What?" Sclerite responded as he quickly rushed outside to see a train leaving the Crystal Empire. "Let that one go! We attack immediately!" Sclerite ordered.

The Changeling soldiers began to rush into the tanks. Others were preparing the artillery and anti-air guns for any pegasi attack.

"Sir? Is it really wise to attack so quickly?" Spiracle asked with a bit of fear. She was clearly worried about him taking her advice as an act of opposition. "We're still recovering from the trip here. I would suggest at least waiting a few more hours."

Sclerite thought for a bit before making his mind. "Spiracle, I accept your opinion that we are in no shape to fight, but we also have to worry about Equestrian reinforcements. If we wait too long, the Equestrians will arrive and we would have to worry about two armies at once." Sclerite responded.

"I understand sir, sorry if I spoke out of line," Spiracle said.

"Don't worry. I always have time to listen to my subordinates," Sclerite responded. He could hear the tanks roar to life.

"There is one more thing sir. Prior to the start of this war. There were spies who temporarily replaced the Princesses of Equestria. A few of them told us that the Crystal Empire is protected by an ancient artifact called the Crystal Heart," Spiracle said.

"Why wasn't I informed of this sooner?" Sclerite asked.

"You were asleep at the time sir," Spiracle answered.

"Alright, now we know what our target is! Good work!" Sclerite said as he went back inside to retrieve the broken horn. "I'm going to join the tanks in this attack. We will find the Crystal Heart and we will remove it from the equation. Now let's get this tank column moving!"

The tanks began to move towards the Crystal Empire in a single file line. They approached the magical shield that surrounded the entire city. The memory of the extremely close victory still clung to Sclerite like a tumor. As the tanks got closer they began to siphon magic off of the shield and poked a large hole. Despite that, Sclerite was the only Changeling in the army that needed to enter through that breach.

There was so much love in the city. Sclerite was at a lost for words and barely noticed an angry mob of Crystal Ponies charging towards the tank column. The Changelings from Queen Formic's Hive rushed to meet the Crystal Ponies in combat. The red Changelings began to feed off of their anger and hatred towards Changelings caused by earlier incidents such as their attempt to drive them off of the hill. The now super powered red Changelings were much stronger than earth ponies and began to push back the crowd.

Despite that, a few still made it through their lines and were either shot down by Sclerite or were ran over by the tanks. It wasn't long before the crowd turned around and ran. Leaving the ones inside the buildings to throw whatever they had at them. The Changelings did not pursue and instead continued focusing on their goal to get at the Crystal Heart. As the tanks began to fire at the attacking ponies in the buildings. Each shot would cause one to collapse, killing anypony still inside.

The group eventually reached the palace. There Sclerite noticed a crystal in the shape of the heart and immediately guessed, that was the Crystal Heart. As soon as his path was cleared he charged for the heart and levitated it to himself. "We have the heart! Now, attention Equestrian commander! I suggest you order everypony to surrender now or the Crystal Heart gets it!" Sclerite threatened as he powered up his horn. Hopefully somepony heard him.

A white unicorn came out through a palace balcony along with a pink alicorn carrying a foal. "Everypony stop fighting!" the white unicorn ordered. "What are your terms?"

"I want you and the empire to surrender unconditionally! Do this and I promise I will show you mercy!" Sclerite called back.

After some whispering between the unicorn and the alicorn. The princess responded with, "we surrender!"

Sclerite immediately fired a bolt into the air which exploded like fireworks, to let the artillery know of their victory. "Stand down!" Sclerite ordered to his troops. As he began to look around at all the destruction that was caused.

There was a lot of work to do. Researching the horn will have to wait.

Chapter 4: Devastation

Flash Sentry followed the guards outside Shining Armor's protective shield. The army marched through the snow covered land in the direction of the enemy camp. The only sounds that could be heard were the hooves of ponies hitting the snow. Suddenly, a loud screeching sound echoed through the air. This caused the army to stop marching and look up in confusion. Even Flash Sentry wasn't expecting anything like this. A moment later, the Equestrian army was covered with explosions. It was as if a volcano had erupted and sent fireballs down from the sky. Nopony had any time to react before they were blown to pieces. Some had even survived losing a limb and were screaming in agonizing pain. Flash looked around to see the ponies panic. Some began to run back to the safety of the shield while others tried to rush towards the still far away enemy position.

The explosions were bright enough for Princess Cadence to see from one of the palace windows. Shining Armor himself stood at the edge of the shield and watched as the explosion killed the stallions. Those who were brave enough to keep moving had been killed by another set of explosions, while many who retreated barely made it back in one piece.

When the smoke cleared, much of the snow was melted, and the field was littered with the bodies of ponies. Other than coat color, there was no way to distinguish any of the bodies.

Shining Armor had never seen destruction and violence on this scale. They had destroyed an entire army without getting scratched. There was no way they can be stopped. He then noticed one particular pony rushing back.

"Flash! It's good to see that you've survived that!" Shining Armor said.

Flash stopped in front of Shining Armor, "I'm sorry sir."

"Don't be, there was nothing you could've done to change what just happened. For now, be glad that you survived and we'll decide what to do next," Shining Armor reassured, trying not to panic.

"Yes sir," Flash said before trotting off.

"Luna is going to have a lot of work tonight," Shining Armor mumbled as he looked back at the hill, the enemy occupied. "There has to be some way up there," he thought to himself.

"Sir! The Equestrian forces are in full retreat. Should we pursue?" asked one of the soldiers.

"No! Let them run," Sclerite said. He was barely able to stand now. The warmth of the tank protected him from the snow but he had pulled an all-nighter to get here and it was already sunset. That mistake was beginning to catch up to him as he collapsed on top of the tank.

"Hey sir, are you alright?" asked one of his soldiers rushing over to him. She placed her head towards Sclerite's heart and noticed that he still had a pulse and was breathing. "I'm getting you inside," she said as she began to drag him into the cave.