The seven mutants were understandably confused by the situation they found themselves in. They'd been pulled off the street, expecting to be locked up and/or experimented on. They were exhausted and wounded, unable to really put up much of a fight. Despite all this, their supposed captors had basically dropped them off in the center of a military base, the only person in sight being Agent John Bishop. He stood before them, holding out his coat to reveal empty pistol holsters.

"As you can see, I am unarmed," He declared, even spinning around slowly while lifting his coat to show he wasn't hiding anything. "My men have gone inside, and while they are monitoring the situation, they are under my orders not to attack you or act in any way that may be perceived as hostile."

Everyone just looked at each other skeptically. Everything about this scenario screamed 'too good to be true'. Deciding that just standing there was pointless, Splinter spoke up.

"Why have you brought us here?" He questioned.

"Because if I hadn't, you would be in police custody right now. Unlike the rest of this city, I do not believe you to be a threat."

"Oh really?" Raph challenged.

"I believe that you and your family mean the city as a whole no undue harm," Bishop amended. "I believe that you all have risked your lives time and time again to protect New York, and even the world. Take tonight for example. Despite the present danger to you and yours, you still did everything in your power to eliminate the threat of H.A.T.E."

"Well... yeah," Mikey replied. "It's what we do."

"And this is what I do," Bishop said. "I help the citizens of this planet, no matter what they may look like."

He took note of Donny's injury, wincing slightly.

"Perhaps you'd be willing to let one of my doctors tend to your leg. We will have to go inside, but I give you my word you will be safe."

The family looked among themselves, then Leo glanced at Hisako. She put a finger to her head before shaking it, as if to say she couldn't read his thoughts. Even so, the makeshift bandages on Donny's leg was growing redder and redder, showing just how serious the wound was.

"...very well," Splinter relented. "But we wish to accompany him."

"I'd expect nothing less," Bishop nodded. "If you'll kindly follow me."

He led the family into the complex, the doors closing behind them.

...

Out at the Utrom Outpost in D'Hoonib space, Kraang was still seeing to repairs from the Triceratons visit. He was grumbling to himself the entire time about the damages the Triceratons inflicted to him and his facility.

"They didn't have to trash the place. I told them what they wanted to know without any fuss. Why did they feel the need to outright destroy my outpost? I just hope my call for assistance went through. I do NOT want to have to finish these repairs by myself."

Just then, a light went off in his central hub, signaling an incoming ship. Kraang maneuvered his hover pad over to the hub, hitting a few buttons before activating the screen. This allowed him to see several Utrom ships coming to the station, all bearing the insignia of the High Council.

"Finally! It's about time someone came!"

He hit the button to open the landing bay, allowing the ships to land. Once they had landed and the bay doors closed, Kraang rushed out to greet them. He went to the door and opened it up, revealing two Utroms in exo-suits and holding high powered laser rifles.

"Sergeant Kraang?" One of the Utroms questioned.

"Yes?" Krang replied. "What is the meaning of this?"

"By the authority of the Utrom High Council, we place you under arrest for conspiring with a known conqueror and threatening the sanctity of an Utrom protected planet."

"What?!" Kraang let out. "You can't be serious!"

More Utroms come out of the other ships, surrounding Kraang.

"Resistance is futile, Sergeant."

"This is preposterous!" Kraang insisted. "I have done nothing wrong! I was coerced by that Triceraton!"

"Save it for the trial," an Utrom snapped, his laser poking Kraang in the back. "Now move."

Kraang begrudgingly moved forward towards their ship.

...

Back on Earth, Donny was laid out on an operating table as a woman tended to his leg. She had already removed the bullet and was in the process of stitching the wound closed. He winced with nearly every stitch of the needle, gripping the sides of the table.

"I'm sorry," the doctor apologized. "This would be much less painful if you allow me to administer anesthetics"

"No..." Donny hissed. "No drugs."

"Alright," the doctor replied, continuing her work.

Outside, the rest of the Hamato family watched, unwilling to take their eyes off Donny. Hisako sat against the wall, muttering under her breath as Leatherhead held her. The croc had several bandages across his back, given to him by another doctor who had made themselves scarce after the job was done.

"Don's gonna be ok, right?" Hisako asked from Leatherhead's grasp.

"Of course he is," Mikey insisted, plopping down next to her. "He's gonna be just fine."

Leo leaned against the wall, turning to Bishop. The man had not left their side and was making substantial efforts to appear non-threatening and cooperative. So far, he was succeeding, and Leo wasn't sure what to make of that. As if sensing his stare, Bishop spoke up.

"I have no intention of moving or dropping the proverbial other shoe. There's no need to stare so intently."

"Just trying to figure you out," Leo replied.

Bishop sighed slightly.

"You still believe I have some ulterior motive for helping you."

"Let's just say places like this bring up bad memories."

"Of TCRI I assume."

Hisako flinched hard, curling up and putting her head in her hands. Leatherhead's grip on her tightened, pulling her closer. Mikey and Raph both got up, putting themselves between Bishop and her, reaching for their weapons as Leo and Splinter did the same.

"Of course, touchy subject," Bishop realized. "My apologies."

"How the shell do you know about That Place?" Raph demanded, a death grip on his sai.

"I've had my eye on you all four some time now," Bishop admitted. "Ever since the fire that burned down the Hamato residence 17 years ago."

"You've been studying us this whole time?" Donny asked.

"In all honesty, I was attempting to get a sample of the substance you know as mutagen. I was informed it was dangerous in the wrong hands, so when a truck of it went up in flames in Chinatown, I had to investigate."

Hisako's eyes darted out to where Donny was, suddenly very apprehensive to the doctor treating him. The doctor looked up and saw Hisako's gaze. As if sensing things were getting tense, she put her hands up and stepped away from Donny. Bishop also noticed this and slowly moved his hands up.

"We have no intention of stealing anything from you or your injured brother. Unlike the doctors of T-"

"Say those initials, and I slit your throat," Raph warned.

"Raphael," Splinter called out.

"Don't tell me to back off, Sensei. We're literally in the heart of this guy's lair, and our brother is in there with a doctor who could do God knows what. I'm not putting the kiddie gloves on."

"Just go check on Donatello, now."

Raph slowly began inching towards the door, pushing it open with his shell. Once he was inside, he stared down the doctor before turning to Donny.

"You okay there, D?"

"I'll live," Donny reassured. "Just hurts."

"She ain't done anything fishy?"

"Nothing. I've been keeping an eye out. It's just medical."

"I give you my word, I have done nothing but try to help your brother," the doctor promised. "Please, may I return to my work? I need to finish closing this wound."

"...fine. But I'm staying right here. You do anything I don't like, they'll be picking up pieces of you for weeks."

"Very well," the doctor allowed, resuming her work.

Raph looked back out at his family, giving a small nod. Leo, Mikey, and Hisako nodded back before turning to Bishop. The man remained as he was.

"Better?"

"If you know about That Place, then you know why we're so cautious about trusting humans," Leo told him. "Especially humans with your kind of influence."

"Understandably so. Having seen the horrors that madman inflicted, especially upon her, your distrust is merited and expected. But perhaps a small piece of information may help to calm your restless spirits."

"What's that?" Leo inquired.

"The madman is currently locked away in one of the EPF's black sites. Even if he regains his memories, and that is a very big if, he will never again see the light of day,"

"That's a little comforting," Hisako commented. "He still doesn't remember?"

"Not a thing. He's a John Doe kept in maximum security."

Hisako let out a long sigh, visibly relaxing. Even Leatherhead seemed a bit less tense at the news. Seeing the two at ease, the turtles all relaxed as well.

"At least we won't have to worry about that psycho again," Mikey commented.

"Thank God." Leo leaned against the wall, running his fingers through his sweaty hair.

"He may no longer be a threat, but he is far from the only one who wishes you and your family harm," Bishop reminded him. "I believe Jack Marlin and H.A.T.E. made that quite clear."

"Abundantly." Leo concurred. "We barely escaped with our lives this time, and the city was almost leveled just to get to us."

"And from the looks of things, the city's not gonna quiet down until they have your heads. That's part of why I brought you here."

"Only part?" Mikey questioned.

"I'll explain the rest after your brother has been given a chance to rest, something I feel all of you are sorely lacking."

"Thanks," Leo replied, finally realizing just how drained physically and emotionally he was.

"I cleared out an old meeting room," Bishop offered. "It has a single door that locks from the inside. I've already sent blankets and a few mats up there so you could rest in some semblance of security."

"Thank you," Splinter replied as he, Leatherhead and the Hamato Siblings got up and went to said room.

...

Mor Gal Tal, a maximum security prison situated in the heart of an icy asteroid on the edge of the known universe, came into view for the ship carrying Kraang. He was strapped in a strange pod with a large metal helmet keeping him in place. When he saw the intended destination, he turned a paler shade of pink.

"No!" he cried out. "Why there?! I didn't do anything wrong!"

"You sold out innocent children to the most war hungry species in the galaxy," one of the guards remarked. "You ask me, you're getting off easy."

"They were going to squish me! Please, you must believe me!"

"Honestly, this is way overdue. Remember his petition to use the unstable mutagenic to 'augment' our species?"

"We could've been great, and you know it!"

He got jabbed with a taser stick, eliciting a cry of pain.

"Just shut up, traitor."

The ship pulled up to the docking bay. Once the bay doors closed, the ship's gangplank lowered and Kraang was escorted off the ship. He struggled with all his might as several prison guards came out to greet him. Among them was the prison's warden, who was red skinned with a bluish scar over his right eye.

"Ah, the infamous Ex-General Kraang," the Warden smirked. "I've heard all about you."

"Then you should know I don't deserve to be here," Kraang insisted.

"Oh I think you do. You're a megalomaniac who only thinks about himself and his own standing. You sold out an entire planet to save your own skin, putting all the Earthbound Utroms at risk."

"Well, Warden Ch'rell?" One of the guards asked. "What should we do with him?"

"Take him to the isolation wing," the Warden ordered. "Perhaps a few weeks in the Box will make him a bit more accepting of his place here."

"Yes sir," the guard replied before carting Kraang off.

Kraang continued to struggle the entire time, screaming about his innocence and his unfair treatment. His pleas were ignored as the bay doors closed behind him. As the guards walked down the hall, approaching Kraang's cell, a flash of light appeared out of nowhere, blinding them. As the light faded, they all blinked away spots from their vision, turning to see a large anthropomorphic tiger standing before them. It was Tigerclaw, now sporting an eyepatch over the eye Mikey gouged out. The Utrom guards didn't even have time to react before one got a laser to the face, the other getting hit with a freeze ray and freezing solid. Tigerclaw then brought his fist down on the guard, shattering him and causing him to drop Kraang. The second he hit the ground, Kraang began scuttling backward, his containment helmet making it difficult.

"What do you want?!" he cried out. "Please, don't hurt me!"

"If I wanted to hurt you, you'd already be hurt." Tigerclaw stowed his guns and picked up Krang, holding him by the helmet. "I'm here to offer you something."

"And what might that be?"

"Payback," Tigerclaw answered, pulling Kraang free of the helmet. "On the five freaks that got you thrown in here. It's not your fault the Triceratons came asking about them to you. It was self-preservation."

"Thank you!" Kraang threw his tentacles in the air. "Finally! Someone who gets it!"

"Yeah, I get it." Tigerclaw rubbed two fingers across his eyepatch. "Having everything you're working for just ruined by a bunch of kids."

"If I'm being honest, I had hoped those Triceratons would destroy them. They've been all Mortu talks about. Five little brats who aren't even of our species, and yet he had the entire system on alert for them. What makes them so special?!"

"Not sure, but they are tough. Getting rid of them isn't gonna be easy."

"Then it's going to take more than just us. We need someone who knows the turtles the best."

All of a sudden, a dark voice called out from one of the isolation cells they were passing.

"The turtles?"

The two paused in front of the door, caught off guard. Tigerclaw glanced at the prisoner info, squinting.

"Who is this?" He questioned.

"The information says someone called 'The Shredder'," Kraang informed him. "He's a Terran."

"Terran?" Tigerclaw mulled over the information, thinking back to the Battle Nexus introductions. "The turtles and their human sister wouldn't happen to be from the same planet, would they?"

"Indeed they are," Kraang answered, an idea forming. "Hold me up to the scanner. I think I can hack to door."

"I have a better idea."

Tigerclaw pulled out his laser gun and shot the panel. The panel shorted out and the door opened up, revealing Oroku Saki chained to the wall. His mechanical arm was gone, leaving only the stump. He was wearing an orange outfit, though most of it was obscured by a metal chest plate locked around his waist. A thick collar was wrapped around his neck, keeping him secured to the wall, and his remaining arm was completely immobilized in a long metal tube that covered his hand. His long black hair hung in his face, and his eyes had a gleam of rage and lust for vengeance.

"So, you know the turtles?" Tigerclaw surmised.

"They stole my daughter, my clan, my honor, even my arm," Shredder snarled, getting to his feet as much as the shackles on his legs would allow. "They threw me in here to rot, to be left in disgrace until I was forgotten."

"Then I suppose you wouldn't be interested in our little plan to take them out once and for all?" Tigerclaw mused.

"Oh I would. I would indeed. Free me from these infernal chains, and I will rain hell down upon them."

Tigerclaw shot at the chains, freeing Shredder from his bindings. He flexed his fingers, then popped his neck, taking in a deep breath.

"Finally."

"We best get going before more guards arrive," Kraang elected.

At that moment, an alarm began blaring, a light going off.

"Bodies discovered in Isolation Ward!" a voice called out over a loudspeaker. "Possible escape in progress!"

"Grop," Kraang cursed.

"Let's move!" Tigerclaw let out.

The three of them made their way out of the cell and down the hallway.

"We need to get to prisoner effects!" Shredder insisted. "I must reclaim my armor, as well as my missing arm."

"Right!" Tigerclaw agreed, drawing a pistol. "And while we're at it, find a body for this one."

Kraang wiggled in Tigerclaw's grasp.

"Agreed! I abhor being carried around like a piece of luggage!"

"Then tell us which way to go," Tigerclaw ordered.

"Do I look like I know?!" Kraang snapped. "I'm a General, not a prison guard!"

Tigerclaw then perked up, thinking of an idea.

"No, but we're about to have a lot of them coming. Very soon."

"Kill them all, but keep one alive," Shredder surmised. "They'll tell us what we want to know, and provide him with the body he requires."

"Exactly," Tigerclaw confirmed with a sinister grin.

...

Several Utrom guards were pouring into the Isolation ward, each armed to the teeth. They approached the doors of the isolation wing, which had been sealed off due to the breach. They all turn to each other and nod before the doors opened up. The second they did though, Tigerclaw busted through and began using his claws to tear through Utroms left and right. Shredder followed close behind, and while only having one arm, still was a capable fighter. He kicked one Utrom aside before grabbing one by the arm and kneeing him in the face. He pulled away the gun and just blasted randomly, shooting down several Utroms. Tigerclaw meanwhile set Kraang down near one of the downed exo-suits as he ran back into the fray, allowing Kraang to pull out the Utrom inside and take control of the body.

"Finally!" He let out, joining in the fight.

Shredder discarded the gun before grabbing one of the Utroms stun batons and bashing him with it. He spun the baton in his hand before using it to smash Utrom bodies left and right. Tigerclaw meanwhile pulled out his bola, swinging it in the air before shooting it out at the head of an Utrom body, tearing it off. When the Utrom inside attempted to escape, Tigerclaw mercilessly squashed it with the spiked ball at the end of the bola.

"Anyone else?" Tigerclaw asked.

Much to his surprise, more Utroms continued to try and stop them.

"My people are too stubborn to give up," Kraang growled. "Cheap fear tactics are useless."

"We have no time for this," Shredder snarled. "We must reclaim my armor and leave."

"Agreed," Kraang said before turning to Tigerclaw. "Get us out of here!"

"Wait!" a voice called out.

The three turned to see a pair of eyes peering through a slot in a cell door. Shredder recognized the eyes immediately, his face becoming cold and indifferent.

"Hun. What do you want?"

"Take me with you," Hun pleaded. "Please."

"You failed me one time too often. It is because of your incompetence that Hamato Yoshi and his worthless brood were allowed to live, destroying everything I had worked for. You can rot in this cell for all I care."

"Cold," Tigerclaw smirked. "I like it."

"Let's go," Shredder told them, prompting the three to take off.

...

Back at the EPF, Agent Bishop looked at security footage of the conference room he'd offered to the Hamato family. Despite the door locking from the inside, the turtles had taken the added precaution of moving the table in the way of the door as a barricade. They had then gathered in a large group on the opposing wall, huddled together as they tried to rest. As he watched them, the doctor who had tended to Donny walked in, looking tired.

"I'm surprised they can sleep," she remarked. "Stuck in an unfamiliar place with potential enemies all around."

"They feel safer together," Bishop surmised. "Besides, no matter how much they try and fight it, their last battle was physically taxing, on top of the mental stress of the entire city actively trying to hunt them down. They can't fight their own exhaustion."

"A fair point. Still, what are we going to do? The people believe we've taken the mutants into custody, but the turtles will not react well if we tell them they can't leave. They don't have any reason to trust us."

"I know. Even so, this may be our only chance at saving them."

"I doubt they will see it that way."

"I know, Dr. Bennet. I'm well aware of what I'm getting myself into."

The two turned back to the monitor, looking in at the sleeping mutants with an air of trepidation.

...

Back in space, a small team of guards took their post in front of the armory, determined not to let anyone in. Suddenly, Tigerclaw's bola shot out, hitting one of the Utroms in the head and pulling him into the darkness.

"Stand your ground, men!" The Utrom in charge of the guards commanded. "We cannot let them escape!"

"How noble," Tigerclaw remarked, opening fire on all the Utroms.

They were mowed down in mere seconds, allowing the three criminals to come out and enter into the armory. Once they were inside, Shredder made a beeline for his armor and arm, placing the latter on immediately.

"Finally," Shredder let out, moving his metal appendage.

One Utrom immediately tried to stop him, but the metal arm shot out, crushing the Utrom's robotic head in its grasp. He then cast the Utrom aside as he donned the rest of his armor. Kraang meanwhile was searching for any upgrades he could find for the body he was using. He found various weapons that he began installing onto his suit

"This is more like it."

"This is an impressive arsenal, but we'll need more than this if we're going to be able to destroy the turtles," Tigerclaw pointed out.

"Our feline friend has a point," Shredder agreed, adjusting parts of his armor so they fit properly. "The turtles and their ilk are nothing if not stubborn."

"Indeed," Kraang agreed. "I think I know of something that just might help. However, we need to get out of this prison if we want a chance at getting to it."

"Where's the nearest transport then?" Shredder asked.

Tigerclaw smirked, then reached into his pocket, pulling out his handheld portal device.

"You're looking at it. Just tell me where I need to go, and we'll be there before you can blink."

"There's an Utrom weapons depot on the other side of the galaxy," Kraang explained. "Take us there."

Tigerclaw input the coordinates, the three fugitives disappearing just as Ch'rell and his reinforcements arrived. When he saw the remnants of the transport field dissipate, he let out a curse in native Utrom tongue.

...

Back at the EPF, the turtles, Hisako, and Leatherhead were all fast asleep, curled up in one massive pile against the crocodile. As they slept, Splinter cracked an eye open, carefully disentangling himself from his children. Mikey felt his movement and stirred, but Splinter gently shushed him, planting a small kiss on his forehead. The orange turtle settled almost immediately, allowing Splinter to make his silent exodus. He quietly opened the door so he could sneak out and closed it just as silently, allowing him to move about the facility.

He checked every corner he came to, dodging the cameras that filled the halls. Years of training and a life of secrecy aided him in remaining hidden, allowing him to search the area.

The first area he found was a barracks, full of EPF soldiers sound asleep. Not wanting to cause any disturbance, Splinter just let them be and moved on. The next thing he found was a lab full of alien technology that was either in the process of being studied or taken apart. He did see a few weapons, but that didn't seem out of place in a place like this, so once more, he moved on. Finally, he reached what appeared to be some sort of information hub, something that piqued his interest. He was about to enter when a voice caught him off guard.

"Unless you happen to have Donatello's tech skills, I highly doubt there's much you can learn in there."

Splinter turned around to see Bishop standing behind him. The man didn't seem upset, or angry by the trespass. If anything, he seemed like he'd expected it.

"I hope I am not prying into anything," Splinter spoke.

"Honestly, I was wondering how long until one of you decided to poke around. Perhaps I can answer any questions you may have. There's a break room just down the hall."

Splinter was hesitant, but felt he needed answers. He relented and followed Bishop down the hall. They entered the break room as Bishop approaching a coffee maker, pouring himself a cup.

"Coffee? I promise, it's fresh."

"Thank you. I must ask, why are you so eager to help me and my family?"

Bishop passed Splinter a second coffee mug, then took a seat across from the rat. He took a deep breath, then began.

"I highly doubt you'll believe me, but everything I'm about to say is true. During the 19th century, a soldier was stolen from the battlefield of New Orleans. He was to become an experiment to vicious aliens who wanted to study our kind like lab rats. However, his life was spared due to the timely escape of one of their other experiments. The soldier was returned to the battlefield, shaken, but not broken. He realized that the world was far bigger than anyone could possibly comprehend, and that there were both benevolent and malicious entities with their eyes on earth. That soldier was me."

"You'll forgive me if I seem... skeptical."

"Understandably so, but I assure you this is the truth. You see, I was not left unaffected by my time with the malicious aliens. My DNA was overwritten with a code that ensured my longevity, repairing damage quickly and preventing aging. It was their way of ensuring their test subjects didn't 'wear out'. Upon realizing my newfound gift, I decided to make use of my now overabundance of time. I formed the EPF to try and establish peaceful relations with any alien visitors who may venture here."

"I am surprised. Not many who went through what you did would be so welcoming."

"True, but I had the benefit of seeing both the good and the bad of extraterrestrial life. As such, Aliens like your Utroms were welcomed, especially when they explained they were galactic law enforcement. They aided me over the decades with incidences such as Roswell, and the aftermath of your Triceratons. In return, I kept information such as your mutation, the presence of mutants, and all the unpleasantness of TCRI out of the media."

"And now that we are no longer secret?"

Bishop sighed again, fiddling with the handle of his mug.

"I'll be honest, the city's not ready to handle you just yet. They're scared, hurt, and irrational. Your family is in grave danger if they attempt to return home."

"Then what do you suggest we do? Stay here?"

"Yes."

Splinter was taken aback by this. Bishop gently waved him down, trying to keep him calm.

"I know this must be a shock, but please hear me out. Your family will continue to be hunted if you remain in the city, and soon, the government will send someone other than me to deal with you. Whomever they send will either capture you for experimentation, or kill you on sight. You've already experienced the first, and I do not wish the second to befall any of you."

"And we remaining here will fix this?"

"It's a start. Once the public has had a chance to recover from the Triceratons and the expansion of their world, we can begin working on reintroducing you to society as protected citizens. Until then, you can remain here as my guests. You'll be free to move about the complex and I give you my word that no harm will come to you or your children. I'll do everything in my power to make your stay comfortable. All I ask in return is your cooperation, and perhaps in time, your trust."

Splinter looked at Bishop, seeing the logic of Bishop's words. His family was in danger, and no amount of hiding would change that. The idea of losing any of them to a lab or to an overeager soldier made his heart skip a beat. Closing his eyes to ward off the imagery, he finally found his words again.

"You make a good point. Still, this is something I need to discuss with my family."

"Of course," Bishop nodded. "I understand this is not an easy choice to make."

Splinter then took his leave, with Bishop secretly hoping that Splinter and his family would make the right choice.

...

Meanwhile, Shredder, Tigerclaw, and Kraang all appeared in a depot. It was a massive steel complex lined with all manner of alien weapons.

"Now this is impressive," Tigerclaw commented. "So, where's that toy you were talking about?"

"This way," Kraang directed.

The three of them moved deeper into the complex, passing shelves upon shelves of Utrom blasters and other such weapons. However, Krang ignored each and every one of them, making his way towards a large set of hangar doors.

"When the Utroms became galactic peace keepers, they decommissioned many of our most powerful weapons. I managed to save a few from becoming scrap, including my pride and joy."

The hangar doors opened up, revealing a massive spherical station with a red circle that resembled an eye in the center of it. Tigerclaw's jaw hit the floor as Shredder's eyes widened.

"Gentlemen," Kraang began. "Allow me to introduce... the Technodrome."