A.N. Welcome to chapter one! The prologue was a bit short I know. But aren't they all? Probably not...Oh well, on with the show. Please feel free to comment at the end, all manner of response is welcome. Enjoy!

Switched

By Lycanpoet

Chapter One

Coming to his senses slowly, Shinji groaned at the bright lights and the white ceiling of the ever familiar infirmary came into focus. Not that he felt bad at all; in fact he had never felt better. Refreshed and revitalised he was starting to think he never should have doubted the bottle blonde doctor. Looking to the side for a clock his gaze stumbled upon the sleeping form of his guardian, draped very unladylike over the chair beside his bed and snoring lightly.

Frowning a little he wondered why she was here. The girls were probably in a similar state as him, so she should be in her office working away like normal. A sneaking thought crept into his mind. Unless something went wrong that is. But he quickly quelled that thought. He felt fine, and he certainly hoped the other two were ok too.

Eyes finding the wall clock, he found it was six hours since the start of the nano...thing. He tried to sit up but felt queasy doing so. His soft grunt of discomfort awoke the captain with a "No more donuts Maya." Comment. Although quick enough, she gained her composure and focus and was up and to his side, gently pressing him back to the bed.

"Whoa there. Don't get up too fast the sedatives haven't worn off yet. You might feel a bit queasy if you try to get up too quickly." She said soothingly, pouring water into a glass on the night stand next to the bed.

'Sedatives? Ah probably to keep us asleep during the nano-thing.' He thought idly.

Hearing Misato shuffling around next to him, he turned to see her looking at him a little uncomfortably. Her mouth opening as if to say something, then deciding against it, and again in a cycle of indecision. Cocking an eyebrow he followed her line of sight down, curious as to what could silence the every bubbly woman.

What he saw, was not what he expected. The blanket covering him looked as if it was tented a little at his chest height. This in itself was not strange, however, when he lifted the cover and peered under, the hospital gown was too in the same condition.

"Shinji..." The raven haired woman started. But cut herself off as he poked the mound in the gown and promptly froze. Shinji's hand started to shake a little, giving a startled gasp as he poked again.

"Shinji...Please don't freak out...There was a slight....complication. You see when Division one started this project; there was only Asuka and Rei. I don't think they anticipated a male pilot. So...you see...they only made one batch of nanites. They aren't very complex; they have to be cultured with certain parameters. These were made to heal the female body not the male." She sat on the side of the bed and took one of Shinji's now feminine looking hands.

Shinji tried to voice dismay at the changes, checking between his legs to try and prove what she was saying wrong. The captain suppressed a groan as the third child fainted dead away.

'Great, just great. Well at least we were allowed to keep Asuka sedated too, that would have just been way too much hassle trying to keep her out and stop her freaking Shinji out before he...argh...she is ready. But now Shinji's awake we can't.' She sighed, still mourning the loss of her drinking time.

*~*~*~*~*~*~*~*

"Report." The deep voice of Commander Ikari rang out through the dark of his office.

Had she not been remotely used to this, Ritsuko Akagi might have flinched or cowered like a new recruit under a drill sergeant. But she held her chin high, keeping her voice clear and level as she read the results of her report.

"The process had ninety-four percent success of the intended result, with the...change in the third lowering the percentage by no more than one point four five percent. We are aware of the miscalculation the first tech division made, and have already begun the process of culturing another batch of nanites to reverse the mistake made." She paused to gauge the commander for any reaction as to his son's misfortune, seeing none, she continued on.

"On to the results of the process, the results of the regeneration and creation of the organs. The Magi calculate that there was a ninety-nine point seven six percent success in the process. We just need to wait on their maturity to gauge full achievement or not."

Before she could add anything else, the commander cut her off.

"Good, see to that they mature quickly. We can ill afford them not to. Make that your first priority, all else is...irrelevant. You are dismissed." He boomed with unquestioning finality in his voice.

Dr Akagi wisely chose not to question her dismissal and left the dark office quickly.

From out of the shadows, Fuyutsuki leaned into the light form his chair. Giving the commander an appraising look. He sighed and shook his head.

"You know she would kill you for this right?" He said in wary amusement.

"She always wanted a daughter." Was the warmly cold reply.

"But she had a son, not a daughter."

*~*~*~*~*~*~*~*

When Shinji came too again, she took a few deep breaths. Freaking out again was not going to help the situation any. The newly turned girl noted that she was alone in the room; Misato had probably stepped out for a coffee or some fresh air. Taking in the new attributes to her body, the former male felt hot tears form in her eyes.

"This is so fucked up." She voiced to the empty room.

Sighing, Shinji shuffled to the edge of the bed dangled her slightly lither legs over the side. She regarded them with detached interest. They were thinner, paler, and to the former boys dismay, more feminine. She lowered her feet to the floor, suppressing a shiver as they met the cold hospital floor. Her legs, upon taking her weight, buckled beneath her, a gasp leaving her lips as the floor rushed to meet her.

Shinji let out a curse as she began trying to bring herself, wobbly, to her foreign feet again. Now up, her body, obviously enough, did not feel her own. Almost as if she had been ripped from her own body; and placed into that of another. Her centre of balance was completely off and she was shaking. Her stance was reminiscent of a toddler finding their feet for the first time.

After making it up to being fully upright again, the newly made girl leaned against the wall for support as she made her way, slowly, in her hospital rooms on suite. Gripping the edge of the sink once inside the bathroom, Shinji stared at the impossible face in front of her. She could not believe it. It was her old face, but it also wasn't. The same features adorned her face as before, although softer, and more feminine. This only made the poor teen's nightmare deeper.

The soft sound of someone clearing their throat behind her almost made Shinji fall again as she lost her grip on the sink and whirled around. But a sort of relief filled her when she saw it was Misato, leaning against the frame of the door and holding what looked to be a bundle of her old clothes.

"Well, there's technically nothing wrong with you. So they can't keep you here. I thought it might be better if I took you home. You know, to have a more comfortable environment to adjust in. I brought a clean set of clothes for you to wear as well." The captain told her in a soothing voice, taking the girl and guiding her to the bed so she could sit down again.

Shinji was grateful to have the captain there with her. It gave her a sense of warmth that someone was worried about her and how she felt. Despite that Shinji blushed as she looked at the clothes next to her and the gown she was still wearing. Looking up at the elder woman she gave a hinting look. Of which Misato Jumped and pulled the bed curtain across with an, "Oops sorry."

Shinji sighed and with great care not to look down or touch herself unnecessarily, she changed into the clothes offered to her. Upon putting the clothes on, it was even more obvious as to Shinji's new gender even though they were boy's clothes. With the shirt tucked in it was more form fitting than it was before.

Shinji snapped out of her thoughts as Misato's hand rested on her shoulder, her guardian giving her a reassuring smile.

"Shall we go home?" She asked.

Smiling back weakly, Shinji nodded and taking the raven haired woman's arm for stability, made her way to the car.

'Let's just pray that Kaji doesn't get Asuka home before us. That way it gives Shinji a bit of time to fortify.' The Katsuragi Woman thought.