Summary: The turtles have spent their whole lives battling the Shredder, but now he is somewhere where they can't touch him: inside Raph's mind, and in control. Who is Ch'rell, and why is he so intent on the genocide of the Utrom? What atrocities lie in his past?

A/n: Kicking off at the beginning of a long story… I'd forgotten how exciting this was! :D

This story is a spin off from the end of the 'Secret Origins' story arc in season 2, when the TCRI building is destroyed and we first discover that Shredder is an Utrom. So this will be set pretty firmly in NT-verse, but (as always) my characterisation is informed by the CGI movie, as well. It will also draw strongly on material from the end of 'Exodus' in season 3, where Ch'rell is put on trial and convicted by the Utrom court (or 'high council', or whatever).

Grammatical note: I'm using 'Utrom' with a capital as the plural as well as the singular. If I slip up and use 'utroms', let's agree to blame it on the characters' bad grammar, okay? I've heard both words used as the plural in the show, so I don't think there's a standard term anyway.

Apologies for this a/n being almost as long as War and Peace. Now on to the story!

Becoming the Enemy

.:…:.

Chapter 1 – The voices in your head

.:…:.

It had been a really long day – and that was an understatement. The several hours that they'd been absent from the TCRI building had actually consisted of three weeks of being chased across the intergalactic universe, fighting Triceratons and Federation troops and despair at the thought of never being able to make it back home. Then they'd been sucked into the Utrom's not-so-virtual reality device, where they'd had to battle the feudal Japanese version of Foot soldiers and defeat the Shredder's ancestor – who, it turned out, wasn't an ancestor at all but the one-and-only, who'd somehow managed to stay alive and annoying for almost a millennium.

And now, just when Raphael thought that things were finally settling down and he could go home, pass out on his hammock, and sleep for about a week, here was the Shredder blocking their way yet again, and saying something about how 'none of them would ever leave here alive'. Again.

Raphael was starting to get really pissed off.

And the Shredder didn't even care that he was going to get them all vaporised by the techno-organic virus in the implosion device that he had dropped – you know, the one that was going to go off in approximately one minute and twenty seconds. No, he was determined to see this stupid fight through to its futile end, destroying them all in the process.

I guess he was pretty upset about missin' out on his revenge, Raph thought to himself as he and his family battled grimly on, piercing Shredder's metal armour with their weapons. The Utrom and their Guardians were all safely on their way to their home world, after centuries of exile on Earth. Raphael was jealous – and Shredder was furious.

His fury blinded him to what was going on, but Raph knew that Don had a plan. Don always had a plan. Sure enough, sparks erupted between the two wires in Don's hands, and leaped towards the torn metal of Shredder's armour. Raph winced and leaned back, shielding his eyes from the bright flashes of electricity with one arm. He listened to their enemy screaming – in anger or in pain, he couldn't tell – but he didn't look up until he heard the almighty crash of Shredder's body hitting the floor.

He knew that even as they lingered, the timer on the implosion device was steadily ticking away, but they'd knocked Shredder down too many times before to assume he was out for the count.

And he was right; but it didn't happen the way he had expected, with Shredder staggering upright and lurching towards them like some kind of demented zombie. Instead, there was a hissing sound as the torso of Shredder's armour opened and slid aside, revealing not skin and flesh but a dark interior. Red eyes opened in the blackness.

Raphael had a very bad feeling about this.

Something came crawling out of the armour.

"The Shredder's… an utrom?" Don exclaimed.

Michelangelo shrieked. "It's the prisoner dude! He's the one who… who…"

The thing opened its mouth and spoke. "Who escaped after causing Mortu's ship to crash on Earth a millennium ago."

Raphael reeled in shock, but he tried to keep his reaction internal. The Utrom in general weren't exactly a beautiful species, but the one who'd crawled out of the Shredder's armour made Raph shiver. It could have been the hideous scarring, or the sight of all those twisting tentacles, or perhaps it was just the expression on its face...

Raph swallowed past his revulsion. "He don't look so tough now. Let's just squish him," he said, smacking a fist into his palm for emphasis.

The tentacled creature seemed to tense, and Raph knew a moment of regret for his words.

It sprung at him with unbelievable force and speed, and he staggered backwards, giving a muffled yell as his face was covered by slimy flesh and grasping tentacles, blocking his vision and gagging his mouth. He stumbled wildly, trying to pull the disgusting alien creature away from his head. "Get it off me! Get it off!" he tried to yell to his brothers, but the Shredder's grip was so tight that the words hardly came out. He was suffocating, and worse, he knew that they must have less than twenty seconds to get their shells out of the building before the whole thing imploded.

He continued to yell and flail around, and the alien started to laugh at him, in a voice that was unmistakably the Shredder's. "What did you say? I can't seem to hear you!" In his panicked state, Raph almost thought he heard the words echoing inside his own mind.

Three-fingered hands grabbed him by the shoulders to steady him, and then Raph could feel a foot planted firmly in the centre of his chest. Leo pushed against him, and grunted as he tried with all his might to dislodge the thing on Raph's head. Even though his ears were covered with slime and god knew what else, Raph could still hear Mikey's yelp.

"Get it off! Or there's gonna be a tiny little Shredder alien bursting outta Raph's chest!"

Blinded, but guided by a lifetime of practice, Raph reached out to whack Mikey firmly over the back of the head. His aim was true, but it was physically harder than he thought it would be. His limbs were growing sluggish, and he felt disoriented and uncoordinated. What was going on? It couldn't be the lack of oxygen, he knew that he could hold his breath for longer than this…

He shuddered as he felt the Shredder-alien shifting on top of his head, and heard a snap of teeth and a yell of surprise from Leo. We don't have time for this, he thought frantically.

"We do not have time for this!" Splinter's sharp words echoed his thoughts. "Leave the Shredder! We shall take them both. Donatello-!"

"Done!" came Don's voice from across the chamber. "I've got the Transmat recalibrated. This bus is leaving!"

It was at that moment that Raphael felt the first tendrils of an alien presence probing inside his mind. My, my, came the Shredder's voice, what do we have here?

This time Raph was certain – the words hadn't been spoken aloud. They echoed inside his skull, thoughts which were not his own infiltrating his consciousness. The creeping horror of it made him freeze. For a few moments he was deaf to the cries of his family, the electronic hum of the Transmat, the ticking of the last few seconds on the implosion device. His world narrowed down until all he could feel was the force invading his thoughts.

Do not stand against me, came the voice, effortlessly brushing past the flimsy mental barriers that Raph had desperately thrown up. Your body and mind belong to me now. You will not succeed.

With a huge force of will, and a spike of panic-fuelled adrenaline, Raph raised his leaden arms and clawed at the thing on his head. "No… Get out! Get out!"

"Raph!" screamed Mikey, "It's time to go!"

What an excellent suggestion, thought the voice that wasn't his. Raphael ordered his legs to move.

Nothing happened. Why was his body failing him? What…

As if sensing everything from the distant end of a long tunnel, Raph felt Leo and Mike grab him around the arms and drag him bodily towards the Transmat, up the stairs and onto the platform of the machine. His legs bumped uselessly on the ground; if his brothers hadn't been holding him up, he would have collapsed. "Get out, get out, get out," he panted, truly panicking now. Then his jaw snapped itself shut against his will, no longer letting him speak.

Thank you for providing me with an escape ticket, Raphael.

Shredder's voice was loud and clear now, as if he were speaking right inside Raph's ears. His body twitched and shuddered randomly in his brothers' grip, and he could feel the vague, uncomfortable sensation of the Transmat as it began to dissolve his atoms for transportation. He thought that he was going to vomit, but for a short flash he was completely disembodied as the machine sent him wherever Don had programmed it to go. When he returned to his body he found himself falling, the alien still clinging tightly to his head, though it had shifted now to uncover his face. Unfortunately, this only meant that he could see the blur of a solid surface that was rapidly rising up to meet him. He hit, hard, and the impact made all thought and sensation cease.

.:…:.

… Consolidate my control… they must not suspect… make them think the fall… I can… the nervous system, and speech centres… yes…

The whispering inside Raph's mind was ceaseless, rising and falling with the constancy of ocean waves against the shore. Stop it, he thought weakly, wishing that he could raise his hands to block his ears, block out the sound-that-wasn't-a-sound. He seemed to be floating in a black void – there was his consciousness, and the whispers, and nothing else. Was he going mad?

"Am I dead?" he tried to say, but the words were only a wisp of thought that hung trembling in the black emptiness. The whispers seemed to pause, distracted, and then a presence turned its focus to him, and he quailed under its piercing regard. There was nowhere to hide. He was flayed open and pinned down, all defences stripped away. The presence could see everything. It knew everything. It was ancient, alien, and infinitely malevolent. And it was inside Raph's mind.

His sanity stretched, and almost broke. He thought he might be hyperventilating, except he didn't seem to have any lungs. He didn't seem to have anything. There was only his mind, and that was held and surrounded by the whispers. They twined through his thoughts like the roots of an old tree growing through rock – implacable, immovable. The presence seemed to know how close he was to shattering completely, for it paused in its questing and remained motionless until his mind had stabilised just enough. Eventually, it 'spoke', and this time the whispers were addressed to him.

I am glad to see you are still with us, Raphael. It does not happen often, but the minds of some beings do snap as they are subjugated. It would have been a shame to have left you as no more than a broken toy. Particularly when you've already been so useful to me. If it were not for you, your heartless family would have left me to be destroyed in that building.

Shredder… Raph's scattered thoughts finally managed to form themselves into coherent words. What… what have you done to me?

There's no need to act so shocked, Shredder's voice drawled from the darkness. This isn't the first time you've experienced an Utrom mind.

Raph did not draw on it himself, but the memory of the creepy mind-meld pods and his experience in Utrom history was pushed to the front of his thoughts. No, he denied firmly. That was freaky as hell, but it wasn't anything like this. This is…

Unnatural? Shredder finished the thought for him. I assure you, it is perfectly natural for an Utrom. My race has become weak and pathetic, with their collective memories locked up in their pods instead of cemented by a physical link. They refuse to acknowledge it, but control is what we are biologically evolved for. We were meant to dominate this universe.

Raphael turned cold. I don't understand. He knew that Shredder was aware he was lying, but the alien explained further anyway, with obvious relish.

Then let me make this perfectly clear, so that you do not waste time fighting it: your body belongs to me. Your mind belongs to me. Your memories belong to me. You will not speak or move or breathe of your own volition. I now control your every move, down to the blink of an eyelid.

That's not possible, Raph thought with as much certainty as he could muster, which was not much.

Not possible? Raphael's mind echoed with Shredder's laughter. Very well. I believe it's time for a demonstration.

.:…:.