This story is also on fimfiction under the name "Return to the Mirror Universe". My account on there is The Spirit of Evil.
Check out the Reflections mlp comic ark (just correct the space in the link, fanfiction's filtering system is so annoying):
part 1: readcomiconline .to/Comic/My-Little-Pony-Friendship-is-Magic/Issue-17?id=21210
part 2: readcomiconline .to/Comic/My-Little-Pony-Friendship-is-Magic/Issue-18?id=21211
part 3: readcomiconline .to/Comic/My-Little-Pony-Friendship-is-Magic/Issue-19?id=21213
part 4: readcomiconline .to/Comic/My-Little-Pony-Friendship-is-Magic/Issue-20?id=21217
Check out "Of King's and Changelings" on Deviant Art. Annoying filtering system so again I can't post the link but a quick google search should let you find it.
Now without further ado, on to the story...
"There is more than one... of Everything."- Unknown
Twilight Sparkle paced her prison cell, wrapped up in her own thoughts. For the last few months, thoughts were Twilight's only real solace. The room around her wasn't much to look at. Thick grey stone walls surrounded her on three sides, and in front of her was a set of bars that gave her a small view of the hallway outside the cell. Small black lamps were mounted on braziers on the far wall of the hallway, casting shadows into the otherwise dark prison. Pacing had become Twilight's routine, so much so that her constant hoofsteps had left a deep groove in the otherwise smooth floor. Thinking was all Twilight could really do in the squalid prison. Her only other option was to talk to her cellmates, and she found thinking to be far more preferable. As she paced, she heard them arguing behind her, like the incompetent fools they were.
"I hate it here! There's no room to fly!" Rainbow Dash yelled in annoyance.
"Indeed! Being cooped up in the dark like this is ruining my complexion." Rarity remarked as she examined her hooves with distaste.
"Oh please, being in here with you makes things even worse. Whenever they bring us food you always try and sneak some of our portion for yourself!" Rainbow Dash said angrily.
"We wouldn't even be in here if it weren't for y'all Rainbow Dash! Ya rushed in to try and grab the diamond when Twilight told you to wait till she disabled the security magic around it! Ah on the other hand was being a team player." Applejack said as she adjusted her black hat.
"Liar! As soon as the security alarms went off you ditched us and tried to escape while we fought the guards! Isn't that right Fluttershy?" Rainbow Dash countered as she looked to her fellow pegasus for support. Fluttershy was sticking her head out of the bars, sneering at every guard that passed. She turned and gave Rainbow Dash an angry look, then went back to what she was doing.
Twilight stopped her pacing as she neared the corner of the cell. Pinkamena was huddled up crying as she usually did when the others started arguing. She pulled out a tissue from her mane and blew her nose loudly. Twilight still had no idea where she kept getting tissues.
Sighing, she pushed her glasses back up to her eyes. She remembered with annoyance that she couldn't magically enhance her vision anymore because her magic didn't work in this stupid prison. The guards had told her it was a spell put on the place by the new Princesses. They had turned good again putting a serious damper on Twilight's criminal exploits... but no more. Twilight smiled as she looked at the line of tallies she had scratched on the wall, marking the days she had spent in the cell. Today her plans would finally fall into place.
"Twilight." Fluttershy called. Twilight turned around and saw a small, purple dragon in a grey trench coat and large shady hat standing outside their cell.
"Spike, right on schedule," Twilight said, "I trust there was no trouble getting in?"
"No trouble at all miss. Most of the guards are off duty, celebrating the festival of Love in the gardens of Canterlot with the rest of the citizens... exactly as you planned." Spike said in his gravelly voice.
"Don't waste time telling me what I already know. Just get us out of here!" Twilight commanded. Spike nodded, and took a big breath in. He released a torrent of green flames on the bars and they slowly melted away until there was a steaming hole as big as a pony's rump. Pinkamena looked up from her crying surprised.
"Hey! Ya didn't tell us about no escape plan!" Applejack said accusingly.
"I tell you what you need to know. Now come on we've got to move." Twilight snapped.
"Woohoo! Free at last!" Rainbow Dash wooped as she flew out of the cell. She was about to rocket down the hallway leaving her companions behind.
"Be quiet you idiot," Twilight hissed, "There are still some guards around." However it was too late. The door at the end of the hallway burst open and five guards rushed in, spears at the ready. They were all buff earth ponies, and Twilight knew there would be no fighting them without her magic. Spike hopped on her back, and she made a run for it to the other end of the hallway followed closely by her cellmates. They reached a small wooden door, which Rainbow Dash tugged at furiously. Locked... naturally.
"Applejack!" Twilight yelled.
"Ahm on it. Stand back!" Applejack bucked hard and the door came crashing down. The guards were seconds away. They angrily yelled "Stop!" and "Halt!" as if Twilight planned to listen. As they quickly entered the room ahead, Rainbow Dash and Applejack grabbed the fallen door and used to barricade the entrance, leaning on it with their backs. The guards outside angrily banged on it demanding surrender.
Twilight saw that they were in some kind of break room. It seemed luck had favored her, and the room was empty. Signs of merriment and fun were visible all around the room. Cups of coffee sat on wooden tables, playing cards were strewn about and the odd comic book lay half read on the ground. To the side a cozy fire crackled warming the hearth. Posters around the room advertised the upcoming festival of Love promising appearances by all of Canterlot's royalty, including the recently rescued King Sombra.
Suddenly a door on the other side swung open, and three guards trotted in deep in conversation. They saw the escapees and immediately took a fighting stance. Twilight noted that one of the guards had a golden badge marking him captain of the guard. The burly earth pony said, "Surrender and return to your cell immediately!"
"Uh oh..." muttered Spike on her back. Twilight saw beside the guards that there was a large bookshelf with a variety of titles. She felt a small stab of regret she wouldn't be able to steal the books and read them at her leisure later. Fluttershy however found a different use for the books. In a fluid movement, she gracefully flew over to the bookcase and knocked it over. The guards yelled in surprise as the bookcase came crashing down on them. Fluttershy laughed with delight as they groaned in pain.
Twilight motioned them onward with a hoof. Rainbow Dash and Applejack abandoned their door and ran after the group. Out of the corner of her eye she noticed Rarity grab the captain's golden badge in her mouth as she ran by. Through the door was another hallway of cells. As they ran past, other prisoners whooped and cheered. Their reputation preceded them as the most notorious criminals in Equestria after all. They turned a corner and found a rickety stair case leading up to a trap door. The door to freedom. Applejack gave it a good buck but it didn't budge.
"Darling some things require a little more finesse!" Rarity said as she put the gold star in her mane and pulled out a bobby pin. She inserted it into the trap door's lock and began to pick it.
"Sometimes we don't have time to do things with finesse Rarity." Applejack grumbled. "And I think this is one of those times." Twilight saw she was right. Three of the guards that had pursued them before now leveled spears at them. Twilight assumed two of them had stopped to help the hurt captain and his companions.
"You're not going anywhere! Put your hooves up or we'll have to use force." the middle guard said with difficulty holding the spear in his mouth.
"But which one of you will get the credit for arresting us?" Pinkamena asked. "I bet your captain will take all the credit. Doesn't that make you... angry?"
The guard on the left turned to his compatriot. "You know she's right Ward Holder, he probably will take credit... again. Boastful jerk."
"Oh please Iron Bar, we all know I'm getting the credit for this. I'm the ranking officer here." the middle guard replied.
"Now wait just a minute there Lieutenant Ward, I played just as big a part as you! And you got promoted yesterday!" the rightmost pony said.
"Why do you deserve credit Locked Tight? I spotted them first!" the Lieutenant replied angrily.
Twilight couldn't help smiling at Pinkamena's handiwork. She always did have a talent for spreading anger and sadness. Behind her she heard the door swing open with a creak as Rarity finished picking the lock. Twilight quickly ran outside followed by her posse. She breathed in the fresh air, enjoying the sunshine she hadn't seen in months. Years if those stupid Princesses had their way.
She felt her magic come back to her, like a switch flipping on in her brain. Spike hopped off of her back, and she levitated her glasses over to him. Things shifted out of focus for a second, and then shifted back to normal as the vision enhancing enchantment she had used on herself came back into effect.
The guards quickly realized their mistake and they charged outside leveling their spears once again. Now that they were outside however, the guards were no threat anymore. Twilight channeled her magic into a levitation spell. The three guards yelped in surprise dropping their spears, as they found themselves being magically lifted.
The lieutenant squeaked, "No fair..." as Twilight shot stunning spells at the three of them. They collapsed in a heap on the ground. However they weren't home free yet. Twilight heard more guards galloping toward the stairs beneath them. She used her telekinesis to slam the trap door shut, and lock it for good measure.
"Yes we're finally free!" Rainbow Dash said as she did loops in the air, enjoying the ability to fly unrestricted. Fluttershy also took to the air and stuck a hoof out in front of Rainbow Dash. Dash didn't see it coming and tumbled out of control trying to avoid the other pegasus, and ended up crashing into a tree.
As Rainbow got up angrily rubbing her head with a hoof, Fluttershy snickered, "Sorry Rainbow Crash!"
"I'll show you crash!" Rainbow said as she flew toward the yellow pegasus. Fluttershy gracefully avoided Rainbow's clumsy attempts to catch her laughing as Rainbow got angrier. She knew she couldn't beat Rainbow in speed, but she could easily dodge Rainbow's kicks and grabs.
Twilight looked on angrily. She had no time for their antics. Already the guards behind the trap door were ramming it hard enough that it was about to give way. "Get down here you incompetent fools!"
The two pegasi stopped fighting and flew down to Twilight and the others. They knew it was better not to disobey her, as they had seen firsthand what her magic could do. Twilight prepared herself, gathering her magic. Mass teleportation was a tricky and limited spell, but she had spent many hours studying it. It would be enough to get them to Canterlot and away from this infernal prison.
A quick flash of her horn and they all stood in the streets of Canterlot. Twilight felt her magic severely deplete, but with the last of it cast a stealth spell around them. A short while later, they were able to sneak aboard a train back to Ponyville.
Twilight grinned at her fellow criminals. "Well girls, at last the mane six have returned to grace Equestria with our criminal genius. But first, we're going to get even with those Princesses for imprisoning us."
"How in tarnation are we gonna do that?" Applejack asked shocked at Twilight's plan.
"Yeah Twilight they're princesses! Plus they've got Sir Discord, Duchess Chrysalis and King Sombra to back them up! I'm all for getting revenge, but maybe we ought to stay hidden for a while?" Rainbow Dash added worriedly.
"Eh miss Twilight I think they're right. I say we go back to selling back end cider for a while so we can make some bits and get back on our feet." Spike agreed.
"Besides, I bet Angel's eager to see me again!" Fluttershy smiled with malice and rubbed her hooves deviously. Pinkamena simply looked indifferent, looking out the train window at the passing scenery.
"I thought you knew me better than that girls!" Twilight said with mock surprise. "What do you think I am, dense? Of course I have a plan. I believe you've heard of the Tree of Disharmony?"