Disclaimer: I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

This story was originally started about nine years ago in an effort to start writing longer material. It sat largely neglected and seldom visited until about two years ago or so and the bulk of it has been written since then.

It was not always a pleasant journey. Bouts of apathy about life in general and episodes of what may well have been depression took a toll on me and weeks would go by where I didn't even look at this. Add a few instances of outright frustration with this story and what should have been done in a year stretched to two or more.

Despite my love/hate relationship with this story I do think it came out well. In this story I have used elements from both the anime and the manga where I thought they fit the scenes better. I actually like some of the subtle differences of the manga characters better. I may have also tweaked a few little things with characters here and there.

It will probably be updated twice a week...I am looking at Mondays and Thursdays for release dates.

Reviews are encouraged and welcome. I try to respond to most when possible. I haven't decided yet if I am going to respond to the reviews that have no reply link at the start of the next chapter or not. It might depend upon what the review said.

With that said, I hope you enjoy my return to the Eva section, it's been a while since I posted anything here. Hope you enjoy it.

Transposed

Chapter 1

On a massive steel gantry platform, deep inside the part of the Tokyo-3 NERV complex that was known as Central Dogma, a beautiful, purple haired woman wearing a short, sleeveless black dress and a red leather uniform jacket sat despondently on the cold metal floor in a puddle of LCL, her bare legs and most of said dress soaked with the putrid liquid.

From a pair of normally soft and warm brown eyes, tears flowed freely leaving them swollen and bloodshot. She didn't care who saw her like this or what they thought of her for it, or what it did to her professional reputation. None of that mattered to her in the slightest right now. In front of her, locked down and restrained in its massive gantry and swathed in cables and vast arrays of monitoring equipment was the giant armoured inhuman creation known as Shogoki. Evangelion, Unit 01.

The Berserker.

The damage sustained in its last battle one month earlier had been repaired and the armour it had shed had been replaced. Damage taken in a battle where at its end the man made monster gained awareness and as the still living Angel known as Zeruel lay twitching and writhing beneath it, ate its S2 organ in a bloody and gruesome display of savage and animalistic butchery. Its massive core was still exposed however, as Dr. Ritsuko Akagi and her staff of technicians tried seemingly in vain to recover the beast's reluctant pilot, fourteen year old Shinji Ikari, who had been absorbed into the living weapon during that last horrifying battle.

The LCL soaked woman crying on the cold steel was many things to Shinji Ikari. Major Misato Katsuragi was his commanding officer, his guardian, and his friend. She had grown quite attached to the young man in the months he had been in her care and the thirty days that had passed since he had been absorbed into the beast's core had been extremely hard on her, adding fresh wounds to her already scarred and damaged soul.

Her job as NERV's Head of Operations gave her enough headaches, worries, and stress as it was, the necessity of having to send children out to fight monsters would do that, but recent events had added to the intense pressure she felt weighing down upon her nearly every hour of the day. She had been finding out just how little she really knew of the overall picture of what went on at NERV and it disturbed her a great deal.

On top of that her other charge Asuka was being exceedingly petulant and defiant again, something that her already frayed nerves were having a great deal of trouble coping with. She was being whiny and resentful at the fact that she had been saved once more by 'idiot Shinji', and she seemed to be totally unsympathetic to his current plight and it had been the source of several very loud and very nasty arguments between the two of them, giving her no respite from the stress even at home.

Asuka didn't seem to care in the least about her fellow pilot and housemate, but as the days since the Evangelion assimilated Shinji into itself wore on, Misato had come to realize just how truly close to her own heart the shy and withdrawn young man had become. Even more so than when he was swallowed up by the Twelfth Angel. She had come to the realization that if she lost Shinji it would be the end of her world and it would destroy her completely. He was the best thing in her life and nearly the only thing that she had to cling to in order to maintain the shreds her own fraying sanity.

When Shinji's father, a title the rotten bastard most certainly didn't deserve and only maintained because of genetics, had summoned the son he had abandoned ten years earlier to Tokyo 3, Misato had been the one who had picked him up and rushed him to NERV. She had truly felt sorry for the kid. All he had wanted was his father's love and approval and what he got was a gruff ultimatum. Summoned only because there was a specific need for his presence, because he was now useful to the bastard who had abandoned him all those lonely years ago. He was told to pilot the Eva or go away.

He was manipulated through his sympathy for a badly injured Rei Ayanami, a girl he had never even seen before, to get into the pilot's seat so that she wouldn't have to. Even after the terrified boy had fought and defeated the Angel, with plenty of help from a berserk Unit 01, Commander Ikari still couldn't muster even the slightest show of pride or gratitude towards his own son. Not even the smallest hint of praise was directed Shinji's way. He had even arranged for the boy to live on his own, for all intents and purposes abandoning him once again and to lodgings that weren't fit for rats to live in. Misato hadn't hesitated and took him into her home, as much to alleviate her own loneliness and her aching need for companionship as for his own well being.

Over the time they had been living together their relationship had steadily grown stronger. Shinji had been slowly becoming less withdrawn and more outgoing, her teasing ways and scantily clad antics serving to loosen him up ever so slightly beyond the embarrassment they caused him and letting him know that maybe someone really did give a damn about him after all in this miserable world. Their relationship had its good days and bad days, a good lot of it due to his battles against the Angels and the ways it affected his fragile psyche, but she was proud of even the small steps forward he was taking and she could only hope that she had been responsible in some small way for it. She knew that she was hardly the ideal of a good role model, but she genuinely cared about him and she wanted to see him become stronger and be able to stand up for himself.

Words couldn't say how genuinely proud she was of him for continuing to pilot Unit 01, something he truly despised doing. While he really did want to protect people he piloted more out of a sense of obligation and a quest for an identity than commitment to a cause, and he continued to do it even though it caused him a great deal of pain. The kid had probably spent almost as much time in the hospital as out of it since he came to Tokyo 3, but he kept getting back into the purple behemoth and saving all of them from the Angels again and again.

He was a lot tougher than he gave himself credit for and he was certainly far braver than he thought he was. If only he could see it for himself. He kept calling himself a coward, but a coward wouldn't keep coming back to the fight and defeating the enemy. Whether he could see it or not, he was a hero. A reluctant one sure enough, but those were the type who often displayed heroism in its truest form. They didn't seek glory for their actions, they only did what needed to be done because someone had to do it.

Misato had come to realize that she could no longer see her life without Shinji in it in some capacity. He really was a good kid and to her own embarrassment she had to admit that he looked after her a lot more than she looked after him. He had come to accept her for who she was, warts and all, though she didn't know how long that would last if he ever saw the worst of her behaviour and he seemed to genuinely care a great deal about her.

The nature of her feelings for him were a source of personal struggle for her at times. She was a surrogate mother, a big sister, and a friend to him, and to be totally honest, if their ages and circumstances were different their relationship would most definitely be something a lot less wholesome. But that wasn't the reality of it. They were a big part of each others lives and it had become apparent to Misato that it was a part of her life she could no longer live without. Perhaps it was just her loneliness talking, but she needed him. He was her family and the fact that he had been lost to her for the last month was slowly and surely killing her.

Up in the control room, Ritsuko Akagi watched her friend through the observation windows as she washed down a handful of aspirin with yet another cup of the horrible, industrial strength, and quite possibly toxic concoction that passed for coffee on the command deck. Their most recent and best attempt to recover Shinji from Unit 01's core had failed and she was tired. Actually, she had passed tired a long time ago and was now somewhere on the far downhill side of total exhausted.

With little success to show for it, she and her crew had been trying for a month to find a way to get Unit 01 to give up its shy and reluctant young pilot and they were running out of options. The telemetry and the sequence of events from their last attempt to retrieve him had left her with no other conclusion than to think that Shinji simply didn't want to come back. After everything the boy had been through she could understand it if that was the case and he didn't want to return. They had placed the weight of the entire world on his slim, untrained and unprepared young shoulders, and while he had managed to carry that weight thus far, he hadn't done so without sustaining significant damage in return.

If he had actually decided to stay within the Eva and thus was able to finally run away for good, she really couldn't say that she would hold it against him. But there were forces at work to whom that outcome would be most unacceptable and although her reasons were different than those of Commander Ikari, Misato had made it painfully clear that she expected her to do anything and everything possible, and then some, to retrieve Shinji from within the belly of the beast that was Evangelion.

'You've gotten way too close to him Misato,' she thought sadly. 'You're his commanding officer, it's your job to send him out to fight… and to die if necessary,… to protect the human race.'

It wasn't that she didn't like Shinji, she did, he was a good enough kid and he tried hard despite the pain and discomfort his battles caused for him and the crippling nature of his past. Hell, if she had known that he could cook like he did she may well have taken him in herself and gotten the better of the two Ikari men by far in the process. But none of them could afford to be too attached to the pilots. She knew that made her sound like a cold, heartless bitch, but it was the hard and brutal truth of the situation they were in.

However, her conscience had been rearing its ugly head for the last month or so. She could have sworn she had beaten it into submission and buried it a long time ago, but apparently it was still alive and well and more than willing to start kicking her ass. After awakening from a long hibernation it had been forcing her to think about all of the things she had done and still continued to do.

Luckily, she was a hardcore workaholic and that usually was sufficient enough distraction to push her troublesome conscience aside, but that didn't seem to be working lately. She had been suffering from some rare moments of clarity about her situation recently and it weighed heavily on her mind. She found herself regretting a great many of the things that she had done under the guise of Project E and one of the things she was beginning to regret most of all was her so called relationship with Gendo Ikari.

She had been overwhelmed by the man from the very start. Her relationship with him filled the void of loneliness that she had seemed to carry within her for as long as she could remember. She had never been good with relationships so it came as a great boost to her that someone as important and as powerful as Gendo Ikari would be interested in her, let alone romantically so. However, she had only been seeing what she wanted to see and by the time she had realized that she was just another of his many tools, it was far too late. She was hooked. Leave it to her to be in love with a man that clearly didn't love her and was only using her for her expertise in his quest to be reunited with his dead wife.

There was no way she could ever compete with that, but his cult of personality had ensnared her just like it had her mother before her and she had no doubt that she too would meet a very bad end when her usefulness to him had run its due course. Had she really been so overwhelmingly desperate for someone to love her, for someone to notice her, that she was willing to not only overlook the things that he was doing but to be an active participant in it as well? How had she managed to sink to such abysmal depths?

Lately, she was really not liking what she saw staring back at her from the mirror every morning. She had been spending a lot of time recently thinking about who and what she had become and the shame was almost more than she could bear. All of the things she had been forced to do and all of the things she had done willingly and without question to aid his cause were beginning to catch up to her and were crushing her soul under their immense weight. She was damned if she knew how to get out from under it now.

One of her worst transgressions among the many she had committed, and the one that seemed to be hitting her the hardest these days, was the way she had treated Rei Ayanami. She didn't know why she had suddenly started to feel such guilt and remorse over her treatment of the hybrid girl. Maybe it was because of her waning love for Gendo and her realization of just what a monster he truly was, and what a monster she was well on her way to becoming. Maybe it was because of the way that Rei seemed to be so unaffected and oblivious on an emotional level, as if she wasn't even aware of her own mistreatment.

Considering the way she had been raised and how her behaviour had been directed and managed through both psychological means and the use of an array of pharmaceuticals, it was little wonder. Gendo had wanted to create an obedient, emotionless doll that would do exactly what he ordered her to do without question, and he had succeeded wonderfully. He had created a life simply so he could twist it to his own selfish ambitions. Something that she had played no small role in bringing about.

She had been so jealous of all the attention he paid to the girl that she ended up treating her with barely concealed contempt, as if she were nothing more than an inconvenient lab experiment that someone else had dumped into her lap. Rei herself had done absolutely nothing to deserve the treatment she received at her hands. She was probably the biggest victim of them all because she suffered at the hands of so many and it was doubtful that she even really knew it. Her newly resurgent conscience had been forcing her to start looking at the situation and the world at large from Rei's perspective. It had given her many sleepless nights and it left her feeling hollow and sickened and horribly ashamed of herself.

'Maybe your way is better Misato,' she mused sadly as she continued to watch her distraught friend. 'At least you still have your humanity. I seem to have misplaced mine somewhere.'

On another walkway far above the control room and the restrained monster, stood a blue haired, red eyed girl, dressed in a teal green and white school uniform. Rei Ayanami usually displayed little in the way of emotion. Despite what people thought of her she did indeed feel emotions, she just didn't quite know what to do with them, or how to accurately identify them, and she certainly didn't know what to do with them. Much of the time she simply had no capacity to care about them. But if anyone were to see her right now they would see an obvious and unmistakable look of worry on her face. She was very afraid for the fate of the one person she could truly call a friend. Perhaps the only real friend that she had.

Almost from the first moment that Shinji Ikari had entered her life he had begun to have an effect upon her. At first she was simply puzzled by it. When the attack of the Third Angel caused her to be knocked from her hospital gurney he had rushed to her aid and cradled her bleeding and broken body in his arms. Then, despite being scared half to death, he agreed to pilot the Eva so that she wouldn't have to. She didn't know why he would do such a thing. He didn't know her or know anything about her, yet he was willing to take the pain and risk his life so that she would not have to.

His accidental groping of her breast had left her feeling…unsettled. Perhaps because she had never been touched in such a fashion before and the sensation itself had been strange to her, though not altogether unpleasant. When he helped her out of the entry plug after they destroyed the Fifth Angel she noticed the warmth of his touch even through the material of her plug suit. It too was not displeasing. She had also smiled for him. Both the smile and the touch had affected her greatly, making her wish to be in his presence more often though she did not understand why.

The day she had asked him to stay and have tea with her at her apartment had been a uncommon occurrence for her. Somehow she felt compelled to be with him. When she burned herself on the kettle and he held her hand under the cool water to soothe it, the feeling was different from anything else she had experienced before. It was pleasant and somehow made her feel warm, even happy. It was all very confusing to her and from that moment on she knew she was no longer the same as she had been. She was starting to actually feel and it was all because of the kindness of Shinji Ikari.

It caused her to spend a great deal of time thinking about her life and where it was going. She felt herself being drawn towards Shinji and away from the Commander. She found herself thinking of him now instead of the man who had created her and given her a purpose in life. She no longer wished to be an empty, emotionless puppet to a man whom she now realized had never truly cared for her as a person, but only as the tool he had created to serve his needs.

Her body may have been created in a laboratory and her soul may be that of Lilith, but she had made them her own. She was not a puppet or a doll or a tool. She was Rei Ayanami, inside and out, and she was beginning to figure out what she wanted. She wanted to live. She wanted to feel. She wanted to experience life and know what it was to be happy and she wanted to discover it all with Shinji.

If only the beast would give him back.

She silently pleaded with it to let him go. In her mind she saw the bestial face of the true monster that lay beneath the armour. There was a part of them that was the same. They were both created of the flesh of Lilith. Her eyes closed in concentration, her mind sought out the purple Eva's consciousness.

'I am you," she began. 'You are myself. You are what used to be me.'

'Yes, you are me,' the beast responded, its voice tinged with annoyance. 'I am what used to be you. So then, why? Why do you interfere?'

'You can't,' Rei pleaded. 'Don't take Ikari-kun away. Give him back to me.'

Inside the core, the beast seemed to consider this for a moment as it regarded the young boy who now fearfully struggled against it, its selfish and self serving disguise as his mother now gone because of the blue haired child's interference. Reluctantly it let him drift away, onward toward the waiting arms of his real mother. Suddenly, the beast transformed its appearance again to that of a beautiful woman with long, dark, flowing hair. That beautiful face though was now marred by a look of deep shame.

'I have been selfish and thought only of myself,' the woman whispered. 'I have let the baser instincts of the beast override me again since going berserk against the Fourteenth and the process of assimilating its S2 organ is affecting my sense of self. I must refocus and maintain myself and my control, otherwise I am jeopardizing everything.' She seemed to pause and gather herself. 'No matter what I may do, the choice ultimately must be his. He is the key to it all. He always has been.'

Rei could feel no malice in the entity's words. The soft voice sounded hopeful, yet sad at the same time. It puzzled her, but it didn't really matter that much just so long as it allowed Shinji to leave if he so chose to.

'Come back Ikari….Shinji…please come back.'

Back down on the gantry walkway, Misato was coming apart at the seams. Every moment for the last month she had hoped and prayed for Shinji's safe return and had drank herself stupid on many of those nights in grief and fear. For the last several hours she had been cursing the name of every deity she could think of because nothing had worked in the effort to bring her Shinji back to her.

She wasn't good at sitting around and waiting for others to accomplish things, especially when she could add nothing to the solution herself. She wanted so badly to be able to do something, anything at all to bring him back, to be an active part of the solution. But she knew that none of her tactical or martial abilities would make a difference here. This was Ritsuko's field of play and she had made it very clear what she expected of her old friend, but she could feel the cold hand of failure and helplessness clawing at her already damaged heart. Nothing had worked so far or shown much promise of success.

She had no idea what was going on with Shinji inside the Eva and that hurt her as much as his absence did. She couldn't imagine it being anything good. The Evangelion was a creation that they couldn't truly control, a reality that it had brutally driven home to them a month earlier when it had messily made a meal out of the Fourteenth Angel. The ugly truth was that they knew so little about the beast they had created, but they had no other choice but to use it. Was Shinji even still alive inside of its core? Was he aware of anything that was going on around him and that they were trying to get him back? Was he afraid? Was he in pain?

"You have to fight it Shinji," she said in a raspy, shaking voice. "You have to fight to get out of there. Don't let it take you away from me. Please Shinji-kun, don't leave me here all alone."

She buried her face in his empty white shirt which, along with the rest of his clothes, had been expelled from Unit 01's entry plug during the latest retrieval effort. Her tears flowed freely and heavily. It wasn't fair. As reluctant and as scared as he was, he was their champion. Their Slayer of Angels. He was her champion. He wasn't the most talented, graceful, or willing fighter, but he got the job done and that was what mattered. Without him, not one of them would still be alive right now.

He was an innocent fourteen year old boy, saddened by the loss of his mother and made lonely and withdrawn by his heartless bastard of a father and those whose negligent care he was left in. He was a gentle soul who was forced to fight creatures he couldn't comprehend, in a weapon he could barely control. He didn't deserve this. Why had that monster taken him away from her? What did it want from him that he hadn't already given?

She raised her tear streaked face and looked up at Unit 01, screaming defiantly at it with all of her pain and rage. "What do you want with him you fucking monster! It wasn't enough for you to eat the last Angel so you had to take Shinji too?! You can't have him! I won't let you have him!" She stood and rushed to the unprotected core and started pounding it furiously with her fists until her knuckles were raw and bloody.

"Give him back to me! Give me back my Shinji!"

"She's out of her beer soaked mind!" Ritsuko exclaimed.

"Dr. Akagi!" Maya yelled. "There's an energy spike in Unit 01's core!"

"Misato! Get the hell away from there! Get away from the core!" Akagi screamed over the intercom.

"The core is glowing!" Shigeru reported. "Energy readings have gone off the scale! It frying all of the sensors."

Before any of them could take any action, the glow flared and Misato was gone, pulled right out of her clothes and into the core. The flash blinded the bridge crew, disrupting the majority of their instruments and sending alarms blaring.

Ritsuko squeezed her eyes shut tightly, then blinked rapidly several times, trying to clear her vision. When she could see again she was witness to a most unexpected sight. First, the naked body of Shinji Ikari was expelled gracelessly from the core, landing with a splash in the LCL and discarded clothing that covered the floor. As she ordered Maya to call for a medical team a much bigger surprise came. Another naked body was pushed out of the core. This one was a slim woman with brown hair.

"Oh my God!" Ritsuko gasped, as she laid eyes on the unconscious form of Yui Ikari.

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