A week ago at a government base one night, inside were scientists and security agents going about tending to their jobs. Inside a room, a man wearing a black business suit and tinted glasses was walking about a few monitors, before speaking to someone working them, “What's going on?”
“We've picked up some strange anomalies coming from New York, sir.” the man answered.
The suited man squinted his eyes, “Is it alien-like?”
“We'll know in a minute,”
The suited man watched the monitor hone in on New York, where appearing on screen was the turtles fighting what appeared to be Purple Dragons, “It's just the turtles. What else is new?” he asked in boredom, when suddenly he spotted a new batch of turtles helping the ones he was watching, “What? More turtles?”
To add more fuel to the fire, he suddenly saw the Rainbooms and their allies taking on the Dragons using their geode powers, along with facing Turtle Hun.
The suited man was lost for words, until he found them, “What is this?” he turned to some troops, “You. Go to New York, and find out all you can about these girls.” he motioned to the Rainbooms.
“Yes, Agent Bishop.” the agents answered, before taking their leave.
Bishop looked at the new turtles and Rainbooms on the monitor and squinted, “Who are you girls? And what is your M.O?”
In the Present time, underground, the turtles of this universe were leading their doppelgangers, the Rainbooms, and their allies through a tunnel.
“So you got a Leatherhead in this world too?” Mikey asked his counterpart excitedly.
“We sure do.” Michelangelo confirmed.
“Does he like to grab others by the faces and shake them like a rag doll?” Donnie asked in worry.
“Not really,” Donatello answered, “I mean sure he has these violent urges once in awhile, but he's actually a great ally. He's just about the only one here I can talk shop with.”
“What do you mean?” Twilight asked.
“You'll know soon enough.” Leonardo answered, as the group entered an abandoned subway station.
“Nice lair.” Rainbow looked around.
“And it's clean.” Rarity admitted.
“Hey, Leatherhead, you home?” Raphael called out.
“Coming!” came a voice.
The group saw walking in was Leatherhead wearing a lab coat and glasses. The Rainbooms and their turtles and allies were shocked, “That's Leatherhead?” Raph asked in surprise.
“He looks so...” Applejack tried to find the right word.
“Scholarly.” Princess Twilight answered.
“Nice to see we got a mutant gator allie here.” Rainbow admitted.
“Actually, he looks like a crocodile.” Twilight corrected her.
“My friends, to what do I owe this visit?” Leatherhead asked.
“Well, Leatherhead, we thought we'd introduce you to some new friends.” Michelangelo began, as the other turtles approached.
Leatherhead blinked in surprise, “I think I may need new glasses, or am I seeing double turtles?”
“There's nothing wrong with your vision, Leatherhead.” Donatello assured him, as Leonardo explained.
“These are alternate dimensional counterparts of us.”
“Hiya.” Mikey waved.
“This is very astounding,” Leatherhead started walking around the new turtles, “Alternate counterparts who come from a parallel dimension?”
“Precisely.” Donatello confirmed.
Leatherhead took notice of the humans, particularly April and Casey, “You must be...”
“April, and this is Casey.” April introduced them.
“Nice to meetcha.” Casey greeted.
“This is Keno, Karai, and Shini.” Leonardo introduced.
“Karai?” Leatherhead asked, as he looked at the young kunoichi.
“Don't the wrong idea,” Karai began, “I'm not like the one you know.”
“It's true.” Leonardo confirmed.
“I am the Fugitoid,” Fugitoid greeted, “And may I present the Rainbooms.”
Leatherhead looked at each of the girls who introduced herself, “I'm Sunset Shimmer.”
“I'm Twilight Sparkle.”
“Applejack.”
“I'm Pinkie Pie!” Pinkie cheered, as she hugged the crocs arm.
“I'm Fluttershy.” the girl whispered.
“Rarity.”
“Rainbow Dash.”
“Starlight Glimmer.”
“Apple Bloom.”
“Sweetie Belle.”
“Scootaloo.”
“I'm Princess Twilight Sparkle.”
“A princess?” Leatherhead gasped.
“Yes. But there's no need for formality.”
“Always modest,” Spike said, “Name's Spike.”
“Same with me.” Dog Spike added.
“Your pets can speak?” Leatherhead asked the two.
“Hey, I am not a pet,” Spike spoke up, “I am an assistant.”
“In all my years this has got to be the strangest things I've seen yet.” Leatherhead said while looking over everyone.
“Well, pull up a chair, because we got a lot to talk about.” Leo said.
And so Leatherhead along with the Rainbooms and their turtles started story swapping leaving both sides surprised.
“So you were founded by the Utrom and turned into this, but instead of experimenting on you they taught you their ways?” Twilight asked.
“Correct.” he confirmed.
“Makes me wish our Leatherhead was founded by our Utroms.” Mikey said feeling bad for their Leatherhead's upbringing.
“But when they left earth in a hurry they left you behind?” Donnie asked.
“Yes. I had been working on a way to build a transmat portal so I could rejoin them, but through so many circumstances I was not successful. So I decided to stay here not only to continue my own work, but so that I don't give into my own animal rages and attack my friends.”
“Deep.” Pinkie gasped.
Leatherhead turned to Princess Twilight, Starlight, and Spike, “And this world you come from Equestria?”
“That's right.” Starlight confirmed.
“It sounds like a very peaceful place.”
“Well, it's not entirely peaceful.” Spike answered.
“Even so, I am glad my friends could introduce me to all of you. Outside from them I don't get too many other visitors.”
Donnie looked over at Leatherhead's lab, “I gotta say this stuff you're working on is very impressive.”
“Thank you, Donatello. I find a calm and quiet environment helps me focus better.”
“It's hard for me to get that when Raph is busy making noise.” Donnie said motioning to his hotheaded brother,
“Me?” Raph asked in outrage, “Mikey's the loud one.”
“Are not!” Mikey argued.
“Are too!”
As the group laughed at their squabbling, Twilight looked at Leatherhead making her think of the Leatherhead from their home dimension, before suddenly remembering something else. Leo took notice of her concern and spoke.
“Twilight, you ok?”
“I'm fine, Leo. But there's something I wanna know,” she spoke up to his counterpart, “Leonardo.”
“Yes, Twilight?”
“That night when we all first met, you guys asked our turtles if they were clones made by Stockman.”
“Yeah? Sorry, but we've grown to suspect stuff like that coming from him.”
“I figured, but my real concern is you also mentioned... Bishop.”
The others hearing that name were concerned, while the alternate turtles and Leatherhead looked edgy, “Yeah, I did say that.” Leonardo confirmed.
“Leonardo, is Bishop... a bad guy?” Twilight asked in disbelief.
“Well, the stuff he's done is bad to us, but he does want the safety of the planet. Basically it's a mixed bag.” the leader admitted.
“He may wanna keep earth safe, but I wouldn't trust him for anything.” Raphael said.
“I'm guessing you have a Bishop in your world too?” Donatello asked.
“Yes, but he's nothing like the way you're describing your Bishop.” Sunset replied.
“So what's yours like?” Michelangelo asked.
Fugitoid spoke up, “Well, when the Kraang Hive Mind was born, the remaining Utroms created the High Council composed of Queen, Rook, Pawn, and Bishop.”
“Wait a minute, your Bishop is an Utrom?” Donatello asked in disbelief.
“Correct,” Sunset confirmed, “And apparently the human body android model he developed was stolen by the Kraang for them to disguise themselves and walk about humans.”
“Which only made them stick out if they traveled in groups, since they all looked exactly the same.” Donnie added.
“The Utroms have kept to themselves for a long time, until the Triceratons were planning to invade our planet to wipe out the Kraang,” Leo continued, “Bishop came to us with the warning of their arrival. Along with helping us take down the Kraang who were trying to raise their old base out of the river.”
“We lost contact with Bishop when the Triceratons invaded New York, but apparently contacted our Fugitoid to come to earth in case something went wrong.” Raph added.
“And boy stuff went wrong.” April confirmed about how the Fugitoid saved them from planet earth's destruction.
“The girls and I first met Bishop when we went to Dimension X to find out the location of the Black Hole Generator pieces.” Sunset said.
“And he became a scout master at Camp Everfree while we were there on a trip.” Pinkie said, much to the other turtles and Leatherhead's confusion.
“Bottom line, Bishop's been one of our best allies when it concerned the Kraang, Triceratons, or anything else alien-like.” Applejack said.
“Maybe, but his constant abiding by the rules and regulations annoys me.” Raph said remembering how much grief he gave Mona when Dregg invaded New York.
“Wow. Sounds like a Bishop we could at least get along with.” Michelangelo said.
“So what's your Bishop like?” Rainbow asked.
Leo spoke up, “Well, our Bishop is a government agent and head of an organization known as the EPF.”
“EPF?” Casey gasped.
“As in the Earth Protection Force?” Karai asked.
“Right,” Donnie confirmed, “ Once during an invasion between the Triceratons and the Federation, Bishop captured us and even Leatherhead with the aim of dissecting us.”
“Good heavens!” Rarity gasped.
“Why would he wanna do that?” Fluttershy asked.
“Bishop is more or less a xenophobe.” Donatello answered.
“Xeno-what?” Mikey asked in confusion.
“A xenophobe, Mikey,” Twilight explained, “As in a person having a dislike of or prejudice against people from other countries. Or in this case, other planets.”
The other turtles nodded, as Leo spoke, “Due to a traumatizing event Bishop experienced many years ago at the hands of an alien race that turned him into some kind of immortal super soldier he's developed a strong distrust over aliens and made it his goal to contain or eliminate any alien-like threats he deems could be dangerous.”
“Yikes.” Rainbow gasped.
“Your Bishop sounds hardcore crazy.” Mikey added.
“That's not the worst of it.” Raphael said.
“What could be worse?” Donnie asked.
“Bishop once staged a fake alien invasion and abduction on the president using holograms and remote control aliens he created through genetic experimenting, just to get the president to continue funding his organization.” Donatello explained.
“What?” The Rainbooms gasped.
“He practically threatened the city and the president just for money?” Rarity asked in shock.
“Sounds like something worse than Flim and Flam would do.” Applejack squinted.
“No kidding.” Apple Bloom agreed.
“Well, that wasn't the end of it,” Leonardo spoke, “The leftover residue from Bishop's experiments fell into the sewer, and anything that came into contact with it turned into a savage mutant beast that spread to any who came into contact with those already mutated by the outbreak.”
“Even Donnie ended up getting turned into a turtle beast from it.” Michelangelo pointed to his brother.
“Oh jeez.” Donnie gasped, as he looked at his counterpart.
“We were forced to work along side Bishop to help create a cure for the outbreak,” Leatherhead explained with a low growl, “But thankfully with Bishop's lab and data from the mutagen, we created a cure for Donatello and the city as well.”
“And Bishop and his agents were there to help us fight the Tengu Shredder.” Leonardo finished.
“Suddenly our Bishop doesn't seem so bad now.” Raph said, and his brothers and friends agreed.
Later on the group was up top on a roof getting some training in, with A.J, Rarity, and Rainbow helping the CMC. After a good long exercise, it was time to call it quits.
“All this training's made me hungry.” Mikey said.
“Ooh, me too!” Michelangelo agreed.
“Me three.” Pinkie added.
“I think we could all use a bite before we head back.” Princess Twilight admitted.
“And check it, there's an opened pizza place down there.” Rainbow motioned to a pizza cafe.
“Well, suit up.” Leo told his brothers, as the turtles and even Fugitoid suited up to look like civilians.
Once the turtles and Fugitoid were dressed in regular clothes and hats or hoods to hide their identities, they all went down and entered the cafe.
They entered a large booth together, as Mikey spoke, “I'm gonna eat so much my shell will explode.” Mikey said excitedly.
“I'd love to see that.” Raph said.
“So would I.” Raphael added.
As they waited for the waitress to take their order, they noticed the other patrons weren't looking up or speaking at all. This got them concerned, until April sensed something, “Guys, I think we should leave now.”
“Why?” Donnie asked, until the janitor walked by the entrance and locked the door.
Suddenly all the patrons up up to reveal they were security agents in disguise armed with blasters, “That's why!” April cried.
“Attack!” Leonardo called, as the group engaged the agents with the CMC and the two Spike's ducking under the table.
“What is this?” Leo asked in shock.
“Someone's staged an ambush on us.” Princess Twilight deduced.
“And judging by these agents, I got a good guess who.” Raphael said.
“Suddenly the room started filling with a gas, and the agents dawned gas masks, “Knockout gas!” Donnie cried, as everyone started coughing before falling unconscious, even the CMC and both Spike's.
When the agents saw they were all knocked out, one spoke into a walkie talkie, “Agent Bishop, the subjects have been secured.”
“Good. Bring them in.”
At the lair, Splinter was meditating, until he saw visions of Agent Bishop with his sons and their friends captured and contained. As Bishop's laugh and his sons and their friends creams echoed in his mind, he woke up in shock, “No!”
Meanwhile Leo groaned, as he opened his eyes to see a light shining down on him, “What the?” he tried to get up only to find himself strapped to a table, “What's going on?” he looked around seeing his brothers, their counterparts, the Rainbooms, Karai, and even April were strapped down onto individual tables.
“Oh, no. Guys, wake up!”
Each of them awoke and discovered the situation they were in, “What is this?” Applejack demanded.
“Are we in an insane asylum?” Rainbow asked.
“Uh, what's on my head?” April asked, as she tried to use her psychic powers, but nothing happened, “I can't use my powers.” she gasped.
“Or mine.” Twilight realized.
“If I could I'd bust out of here.” Applejack said.
Karai tried focusing, “I can't shift form. These restraints seem to be blocking my shapeshifting.
“Look over there!” Mikey cried while motioning to the right.
They saw all their weapons, the girls geodes, and the turtles medallions on a table, “How'd they get over there?” Pinkie asked.
“Guys, you're awake!” Starlight's voice came.
They looked over seeing Starlight, Keno, Casey, the CMC, and Shini locked in a cage together, “Are you guys all right?” Leo called.
“We're fine. All things considered.” Shini answered.
“Where's Fugitoid?” Sunset asked in concern.
“And Spike?” Princess Twilight asked, as both girls wondered where their dogs were.
“Over here!” came voices.
They looked over and saw Fugitoid himself strapped to a table facing upward, and both Spike's in individual cages.
“Get us out of here!” Spike barked.
“I am not liking this.” Fugitoid feared.
“When I find out who's punking us I'm gonna take my foot and shove it so hard...” Raph was cut off by another.
“Save your threats. They won't do you any good.”
“No.” The alternate turtles gasped.
Walking into the light was Agent Bishop, “Welcome, Turtles. And Turtles,” he motioned to both turtle teams, before turning to the girls, “And a big hello to you, Rainbooms.”
The girls gasped, “Is this Agent Bishop?” Fluttershy asked the turtles nervously.
Bishop answered, “You're correct, Ms. Fluttershy. Now what say we have a little talk?” Bishop smirked.