Authors Notes- Ok, working on the assumption that Shinji's room has a window. I can't remember and I can't find a copy of the floor plan anywhere (well, one, but it did not seem accurate). If anyone knows the layout of the apartment better, any help you could give would be appreciated. Thanks to my pre-readers and everyone who reviewed.

Disclaimer- I do not own Neon Genesis Evangelion or Jekyll and Hyde.

It had taken a little work, but Keel had managed to get Shinji's full medical files, including the data related to his piloting gathered by Doctor Akagi. She managed to convince one of Doctor Akagi's assistants that it necessary to properly evaluate the children. Of course she had requested the files for Pilots Ayanami and Sohryu, in order to keep up the illusion.

Ignoring the files for the first and second children, Keel immersed herself in the data from all the tests that had been run on the third, every blood sample, MRI, all the data gathered from the synch and harmonics tests, and the psychographs from all Shinji's battles.

None of the information was necessary to implement the treatment. That was what made it such an extraordinary breakthrough. The nano-machines were self guiding, making their decisions independently, but the data was necessary to determine whether or not the treatment had been successful.

The files about Shinji's past were quite interesting, especially considering his abandonment by his father. A facet of life she shared with the boy, though he became weak because of it. She, on the other hand, had grown stronger. Her will was more resilient than anything the world could throw at her.

Personally, she would have preferred someone with a more pronounced condition, where it would be much easier to notice the changes, but the need for secrecy made that option impossible. Shinji's social detachment would actually prove useful, as no one would notice the changes until it was done.

And if something went wrong? Well, it was Commander Ikari's fault that she had to resort to such measures. Almost fitting that the first patient should be his son. A harsh rationalization, she knew, but it was all the reason she needed to continue.

She looked up at the dozens of schematics of the nano-machines that adorned the walls of her apartment. Schematics for a machine built from the remains of the eleventh angel, programmed with artificial intelligence modeled on the Magi supercomputer. A machine beautiful in both its simplicity and its complexity.

Machines that now swarmed in the bloodstream of Shinji Ikari.

She had not told him the exact nature of the treatment. The boy would probably faint if he knew that millions of angel-based machines were drifting through his body. All he knew was that she had injected him with a medicine, and that he had to ingest a catalyzing agent to put it into action.

Keel smiled, leaning back in her chair. If everything continued as planned, Shinji would be ingesting the final part of the treatment: a second dose of active nano-machines suspended in LCL, which would activate the dormant nano-machines spread throughout his body.

Now the die is cast, nothing left to do.

Time alone can prove my theories true.

Show the world…

* * *

Kaji smiled, leaning back in his chair. So far so good. If everything continued as planned, Doctor Keel would be too busy working with the children to have any thoughts of retribution against Ikari. It wasn't that he cared about the Commander's life, in fact he wouldn't mind being the one to put the bastard out of his misery, but the old men still had some use for him, and until he had more insight into what was going on, he would keep up the façade of the obedient little spy.

Having Chairman Keel's daughter on the Nerv payroll had been an unexpected complication. Even Keel himself had no idea that his offspring had been transferred from Britain to Tokyo-3, at least until Kaji had informed him of the development. The Chairman had shown little interest in the news, outside of inquiring on her well being.

The best thing for the good doctor, would be to keep her so busy that she would have no time to devote to additional schemes, and giving the children a psychological assessment would be time-consuming for a team of psychiatrists. He was glad Ritsuko had made the passing comment on the mental stability of the pilots, which had made it much easier for him to suggest getting them a therapist, 'jokingly' of course.

Still, he genuinely hoped Keel would be able to find some way of helping the kids. They had already dealt with so much in their short lives, and needed someone to help them.

He shut down his computer, not bothering to save the game which made him appear to be goofing off at work. He put on his jacket and grabbed an umbrella before turning off the lights and locking the door behind him. There was a good chance it was going to storm tonight.

* * *

Shinji turned on his desk lamp and pulled out the journal the doctor had given him. He needed to take careful notes of everything he felt, emotionally and physically. He had no idea what she wanted, but he didn't want to make any mistakes, so he was going to try and record everything he could think of.

He took a deep breath to calm himself, and prepare for what was to come. Doctor Keel had warned him that he would feel a momentary elevation in his body temperature, perhaps a little pain in his extremities, but that it would pass after a moment. But a little pain was a small price to pay if it would help him get over his chronic lack of a backbone.

He looked back at his door, half expecting Misato to slide it open and check in on him like she had so many times before. He had never had anything he wanted to hide before, and for the first time he wished he had installed a lock on his door like Asuka had done on hers. He listened, and heard nothing but silence. He shook his head and pulled a small vial from his bag. Asuka was almost certainly asleep by now and Misato was probably still passed out on the kitchen table with a Yebisu clutched in her hand.

He sighed. There was no point in putting it off any longer. He had already made his decision and the doctor had injected him with the first half of the treatment. She had told him to wait at least five hours to allow the formulae to evenly distribute through his body before ingesting the catalyst. He looked at the tiny plastic vial, the liquid inside glowing a dull but deep red. A label on the side gave the volume and name of the contents.

Steeling himself, he pulled the cap off. Taking a page out of Misato's book, he downed the contents in one swig, only instead of a ecstatic whoop, Shinji began to cough on the foul-tasting liquid. I Probably would have done the same if it had been a Yebisu, he though, and picked up the pencil.

11:58 P.M. It is done. I have consumed 10 cc's of formula HJ-7. Salty, metallic taste, like LCL. It stings my tongue. Warmth spreading quickly through my body.

Slight feeling of euphoria. Lightheadedness.

Shinji chuckled lightly as he leaned back in his chair, almost tipping himself over as he enjoyed the giddy sensation. He pulled himself upright as the dizziness passed and, grinning like an idiot, continued writing.

No noticeable behavioral differences.

Shinji could really feel the heat now. In fact it was getting uncomfortably warm. He stood, walked over to the window and opened it, enjoying the cool night air. It was cloudy tonight, and he could smell the impending rain upon the breeze. A little lightning, and this would be perfect mad scientist weather, he thought.

As if on cue, there was a flash in the distance, followed shortly by the low rumble of thunder. Shinji suddenly had the urge to cackle maniacally, but wisely ignored it. The last thing he needed was Asuka to stomp in and beat him senseless.

Asuka… He was still ashamed with himself after treating her the way he had. He couldn't even think about her without feeling regret. Asuka, I should have said something sooner. I'm sor…DAMN IT! She's right! I am spineless! I can't even think without apologizing! Well, if everything worked out the way the doctor said it would, that wouldn't be a problem anymore.

How will it be? Will I see the world though different eyes?

A sharp pain in his left arm caught Shinji by surprise, nearly driving him to the floor. As he looked on, his left hand began to shake, the muscles in his arm twitching uncontrollably.

My god… What's this?

His fist was clenching and unclenching rapidly, he tried to force it open but the pain in doing so only made the worse. His chest was on fire as his heartbeat began to echo in his ears.

Something is happening. I can't explain.

Something inside me, a breathtaking pain,

Devours, consumes me, and drives me insane!!!

He cried out in agony and… rage?… raising his hand into the air as the clouds rumbled and roared, drowning out his voice. It clenched into a fist one last time as it brought itself down onto his desk, right on top of a picture of Asuka, Misato and himself, shattering the glass. His hand swung across the desk, knocking the journal and everything nearby to the floor.

Shinji started to laugh and scream at the same time, but he was silenced by another wave of agony shooting through his body.

Suddenly! Uncontrolled!

Something is taking hold!

He no longer had any influence over his left arm, the cramping and twitching slowly spreading upwards and into his body. He fell to the floor as the pain knocked his knees out from under him. His stomach churned, and he felt as though he was going to be sick.

Suddenly! AGONY!

Filling me! KILLING ME!

He managed to crawl on his knees using his one good arm to drag himself out of his room and into the bathroom. The pain was now like a knife in his gut, a burning agony spreading along his bones and across his skin. He couldn't get enough air, and his vision slowy began to go black, and he felt as though he was losing himself to the darkness.

Suddenly, Out of breath.

What is this? Is this death?

His hand grabbed the countertop, pulling himself up to stare into the mirror.

Suddenly, look at me.

Can it be?

Who is this …creature… that I see?

There was a hissing intake of breath as he stared at his reflection. "Free…," he breathed.

He laughed. A low, quiet rumbling from the depths of his soul, echoing through the small room.

The click of a lock being turned grabbed his attention . It came from down the hall. He darted back to his room and headed for the open window. Stopping to grab the journal, he made one final note, muttering the words to himself before shoving the journal into the satchel. Looking up, he winced as the bright light of the lamp struck his eyes. He smirked as he reached for it, "Sorry. I forgot to turn off the light…"