Author's Note: This is an idea that I've been thinking about for a while now and i'm kind of glad to be doing it. In the episode "Secret Origins" Raph mentions they were in the alternate universe for three weeks, from what I can tell the turtles and Honeycutt were on the run from the Triceratons and Federation for maybe a day or two so that means they spent nearly three weeks in the Triceraton Prison. I wondered what the turtles went through while in prison, so i'm going to show my verson of what went on during that time. Note that I've taken a couple of quotes from the episodes, so I hope no legal issues happen. Anyway here it is, Enjoy.

Chapter 1: First Night

Nothing but silence filled the long cold halls as the four turtle brothers were marched down a corridor with many cells on each side. After stealing away on the Triceraton's ship to rescue Professor Honeycutt the brothers encounter a problem when the hull was breached, draining all the air in the room they were in. They only way they managed to survive was by performing a breathing meditation that slowed their heart rates, allowing them to drag out the air they managed to gulp up. Yet what followed was something they wouldn't have expected.

Being found by the Triceratons the turtles then found out that they didn't breathe in oxygen but a mixture of Nitrogen and sulfur. This unfortunate discovery caused all four brother's lungs to burn and choked them which rendered them defenseless. They were captured and stripped of their weapons in their weaken state. They managed to survive when they were given convertors which let them breathe in the atmosphere. Now they were sent to prison. After being cuffed and branded they were being marched to their cell.

One of their guarded escorts stopped them in front of a cell and slid a keycard through the reader, which opened the door. They were then roughly pushed into the cold, dingy room that would house them for an undetermined time.

Raph was the last one to be pushed in but had to make a comment which nearly earned him a beating. Luckily he saved himself, "Your boss wants us alive." The emerald turtle smirked, thinking he had one upped the guard.

Just then the guard held up the key card and pressed a button, all of a sudden the marking that was branded on them started to produce electricity, which elicited a cry of pain from Raph, who was knocked back into the cell. His brothers were by his side as the effect stopped.

Their guard looked at them just as the door was closing, "I can make you wish you weren't!" and with that the doors shut, locking them within.

A few seconds passed and the glow of the cuffs shut off; freeing their hands, much to their relief.

"You alright Raph?" Leo asked as his younger brother was helped to his feet.

"I'm fine," he grumbled and walked towards the cell door. "Just wait until I get my hands on those dino breaths."

"There's no point in it Raph, we're trapped," Leo responded, trying to calm his brother.

"No point? Leo are you blind?" Raph turned to face his brother in disbelief. "We're in prison! We have to get out of here!?"

"But we're in a situation where we have no idea exactly where we are or any plans on how to escape," the leaf green turtle tried to calm things down. "We're basically blind here without a guide. The best thing we can do is wait."

The red clad turtle only growled as he turned stomped off as far as the cell would allow him, obviously dissatisfied with their current plan.

"Fascinating," All eyes turned to Don, who was looking at the cuffs that were locked onto his wrists.

"What do you have Don?" Leo asked his genius brother, thinking he found out something.

"From the looks of it these cuffs act as if they were a part of our skin," The purple clad turtle announced as he continued to look at his wrists.

"How can they be if our wristbands have them on?" Mikey asked out of curiosity.

"I say it that way because there's no opening to try and slip them off, almost like they were sprayed on, but they act like they're their own object."

"Which means?" Raph asked as he joined the rest of his brothers. Clearly they didn't get what he meant at all.

"We're wearing cuffs that look as if they were tattooed on."

"Well that's perfect," the emerald turtle responded.

"And apparently it uses a strong magnetic pull that binds our wrists together."

"Which means?" Leo asked.

"They're like magnets, but with a tremendous pull which no one can stop."

"Well what about…I don't know what to call these," Mikey asked as he showed his right shoulder, which had the strange branding mark on him.

Don then glided his hand over the mark, studying it more closely. It was a surprising thing when the olive green turtle's hand felt like he was touching Mikey's skin. "Wow…it's like…a tattoo."

"Really?" his three brother's eyes raised.

"Yeah, there's no way to remove it," Donny responded as he tried to chip a corner, seeing if any part of the tattoo could peel away, but no result.

"No need to guess on what it can do," Raph folded his arms, reminding them of what happened not so long ago. "That shock hurt a lot."

"Yeah," the purple clad turtle responded as pressed a hand to his chin and paced in the cell. "These tattoos are obviously a way to control the prisoners. From the looks of it just a few seconds with it activated could subdue anyone."

Mikey then chuckled as something crossed his mind, "Just to think, we're teenagers and have tattoos. We're just like human teens."

The sea green turtle laughed a bit from the comment, but stopped as the seriousness of the situation returned as his three brothers glared at him. Obviously this wasn't a time for jokes.

"Ok, now that we know what we're working with, how do we remove them?" Leo asked, all eyes on their genius brother, hoping for an answer.

Unfortunately he shrugged, "I have no idea."

That caused them to let out a frustrated sigh as an uncomfortable silence filled the room. Now they were back at square one. They now know of their limitations in prison but now they lack the knowledge on how to remove them. The subject was then dropped as nothing else could be added in.

It was then they looked around their cell, getting a good idea of the place they were staying. The cell was fairly big, had a dirt floor, and horizontal pieces of metal sticking out from the walls.

"So…are these supposed to be our beds?" Mikey asked, looking at the metal that was sticking out.

"Maybe," Leo responded, looking at them as well.

Mikey sat down on the so called bed, silently hissing at how cool the surface was. This was where they were going to sleep on, and there wasn't that much of a choice. It was either this or on the dirt floor. "This is going to be hard to adjust to," Mikey said as he laid down, testing it out. It only took a second for him to groan, "Man, this can't be how they treat us."

"Well it is, and it's not going to get better," Raph grumbled as he sat on his bed, across from Mikey.

"Might as well make the best of things," Leo said as another silence followed. He then turned his gaze to his second youngest brother, seeing him sitting on the ground, shell against the wall. He was staring into nothing, apparently deep in thought. "Something eating at you Don?"

"It surprises me that the Prime Leader wanted us alive," the olive green turtle responded. After the turtles were given the devices that allowed them to breathe there was a moment where they had to try to recollect themselves, which made them weak and easy to capture. Their senses were off a bit as it took a bit for the burn to leave their lungs and for their breathing to get under control. They managed to overhear the captor that had their weapons talking to the Prime leader over a comm. And they managed to hear that they were to be kept alive, surprising them all.

"I know…I mean we never met the guy but he let us live, why is that?" Leo responded, puzzled at the same fact as well.

"Maybe…" Mikey sat up, thinking of something and inputting it. "Maybe they found out that Honeycutt knows us."

Donny snapped his fingers after hearing that, "Of course…" he stood up as the others looked up at him.

"What is it?" Raph asked.

"They must have found out that we have a connection with the Professor and-"

Raph cut his brother off with a growl, "We're being used as leverage…Those good for nothing Dino breaths are using us to force him to make that teleportal!"

"And there's nothing we can do about it," Leo responded with his arms folded.

A loud thump sounded as Raph punched the door to their cell, "We have to get out of here…somehow."

"I know Raph, but sadly as I must say I think it should wait, at least till tomorrow," Leo tried to calm his hothead brother down.

"Fearless, did you forget where we are and the situation we're in!" The red clad turtle turned to glare at his brother, irritated that he was being told to settle down and not to attempt anything for the rest of today. "Please enlighten me as to why we should sit on our shells!?"

Leo then turned his head as a soft snore could be heard, they all looked at Mikey's sleeping from. Somehow the orange clad turtle managed to sleep on the hard beds they were provided. Laying on his plastron they could see him using his arm as a pillow.

The sight of their sleeping brother seemed to have made them all realize all the ignored fatigue that built up inside them. "All that running the past few days must have caught up to him," Don said as he let out a yawn. "And us."

Leo then looked back over at his brother, "It doesn't do us good to plan something if we're exhausted."

The emerald green turtle said nothing as he let out a heavy sigh, then walked over to one of the beds and sat down on it with his shell against the wall. Leaning his head back, so that it was resting against the wall he closed his eyes; now intending to sleep the best he could. Years of sleeping in a hammock made it easy for Raph to sleep in uncomfortable positions that most people would find impossible to sleep in. So now he was sleeping sitting down, shell and head against the wall.

"Well…I guess we should turn in for the night…or day…whatever time of the day we're in," Leo turned to his remaining brother who's awake.

"Yeah, I agree," Donny responded as he turned to his own bed and climbing on, groaning at the hard surface. Deciding to take a page from his younger brother's book the purple clade turtle used his arm as a pillow. Even as he did this he still wasn't comfortable, so he had to keep changing positions.

Leo watched as his Genius brother try to get comfy on the bed, then looked at his two remaining brothers, watching as they slept. He took a minute to make sure they were fine before he could go down himself. Even though they were locked up he still played the big brother and made sure his younger brothers were good before taking care of himself.

Seeing as they were alright Leo let out a tired sigh, true he's exhausted, but unfortunately he wouldn't be able to get to sleep right now. His sprit felt out of focus and he needed to center himself. So moving over to his bed, the blue clad turtle sat down on the dirt floor and folded his legs, assuming lotus position.

Closing both eyes Leo let out steady breaths and concentrated, and soon he could feel himself disconnect from his body, falling in a meditative trance. There was nothing but silence, except for the occasional light to heavy snores coming from the turtles as they rested.

Today proved to be a hectic and horrid day. Their friend, professor Honeycutt was kidnapped, they were almost killed by being deprived of oxygen, then nearly choking on a new atmosphere, then being cuffed, marked and imprisoned by their enemies. If the four brother thought their time couldn't get any worse, they were wrong.

A/N: I hope you like. Now I want to say there's a reason for this story but for now I want to keep as much details underwraps. But for now I hope it was a good chapter, I have some creative things planned and there's a lot to come. Although this is going to be a short chapter story. Till next time.