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

Transposed

Chapter 2

Office of Gendo Ikari

In an instant his world had dramatically changed. From his usual pose, hands folded under his nose concealing his mouth and elbows resting on his desk, he watched the footage of the incident again for perhaps the tenth time, scarcely able to believe what he was seeing. It was a most unexpected turn of events, but one that was welcome nonetheless. It seemed that his carefully planned scenario would no longer be necessary. He had what he wanted and it was better than a hopeful merging of souls. His Yui was here, alive and in the flesh.

However, if there was one thing that Gendo Ikari had learned throughout his years of manipulations, political wrangling, and the fight against the Angels, it was to never, ever, take anything at face value. He was no stranger to tricks and deceptions and he would temper his joy at his wife's reappearance until he was sure that it wasn't a ruse. He could feel it in his bones that it was genuine, but he had to be sure.

Both Yui and his son were in isolation in NERV's medical complex and would stay there until every possible test could be done to confirm that it was really them and not a manifestation of an Angel. Only when it had been proven that there was no doubt to their identities and that there was no contamination present would he accept what his heart was telling him must be true. It had to be true.

"Fuyutsuki," he said to the older man standing next to him. "I want you to personally oversee and review the tests. If there is anything that seems off, even in the slightest, inform me immediately."

"I thought you would be wanting to oversee things yourself," the Sub-Commander said, a little surprised that Ikari wasn't going to look after this personally.

"I need to formulate an explanation that I can sell to the Committee," Gendo answered, his mind already working on the problem. "Their only concern will be the viability of Unit 01 and how the current situation will affect the Instrumentality Project. I must confer with Dr. Akagi about Unit 01's status before I meet with them."

"As we both know, SEELE will already know about what has happened before you tell them," Fuyutsuki reminded him.

"Indeed." The Commander stood to leave, reflexively pushing his glasses back into place. "Increase the security around Yui. I doubt that SEELE would attempt to do anything to her, but we must take every precaution."

As Ikari left the office, Fuyutsuki could only shake his head in disgust. "Not even a word of concern about your own son or Major Katsuragi."

Fuyutsuki used the walk to the medical facility as an opportunity to reflect on his affiliation with Gendo Ikari. When he had initially joined him in this mad scheme it had been out of fear of death. He had threatened to expose SEELE and the cover up of Second Impact and Gendo had made it very clear that such actions would most likely cost him his life. At the time Fuyutsuki didn't care, and he didn't particularly care for Gendo either, but he had allowed himself to be swayed.

As it turned out he really hadn't been brave enough to sacrifice his life for the truth and the scientist in him had been enthralled by all that NERV's predecessor, Gehirn, and Project E were. The scientist in him had sunk its teeth into the project and all that it entailed and it had ensured that he would be forever caught in Gendo's web. Over time, he had buried his conscience and accepted what he had chosen. They were all going to die in the end and there would be no one left to damn him for his participation in this madness.

He had even gone along with Gendo's plans for his own version of Instrumentality. He sometimes wondered why he had done so because the only person who was to derive any true benefit from it would be Gendo himself. He supposed it was just his own weakness that made him go along with it, after all, he had already sold his soul to the devil that was Gendo when he agreed to join up, thus ignoring his principles and morality in the process.

He couldn't help but wonder what Yui's reaction would be to everything that they had done. She had allowed herself to be taken into Unit 01 in order to protect her son's future, which could only be done by defeating the Angels. He wondered if she had done it to thwart SEELE from attaining their true goal of becoming god, despite the words they spoke otherwise of engaging in this to rid mankind of its suffering. She had never openly shown much in the way of opposition to their plans, but he felt that she had never been entirely behind the idea either. At least, she had not been as zealous about it as their masters at SEELE seemed to be and she may have had a somewhat different view on how and what Instrumentality was and how it should work. Maybe she was just more focused on her work in creating the Evangelion.

The fact that Gendo had abandoned Shinji and was working towards Third Impact himself, although for a different reason, wouldn't sit well with her. She would be horrified by it. He knew that she had loved her son more than anything else and she had hoped that he would grow into a strong, confident young man. What Gendo had done to Shinji, from his abandonment on through everything that had happened since he had summoned the boy to NERV, was unpardonable. Fuyutsuki doubted his participation in that scheme would be received any better by her and it made him feel even more ashamed of the submissive role he had taken in it all.

He had been very fond of Yui when he took her on as a research assistant, and while he had no illusions of ever being lucky enough to form a more intimate relationship with her, he had still been appalled and more than a little hurt and jealous when she told him that she was seeing Gendo. He had known from the start that the man was nothing but trouble.

He knew that her return was going to cast some wide ripples across the proverbial pond. None of the pivotal players in this apocalyptic game would be left untouched by her reappearance. Much of what Gendo had done, the lives he had impacted, was all for his goal of reuniting with Yui. A lot of people had been used and abused in the course of his scenario and some of those people would be scarred for life. He thought of the pilots and Dr. Akagi specifically in that regard. He also knew that SEELE would be all over this. They were on the edge with the old men as it was, but if anything else happened that they thought might put their plans in jeopardy there would be some serious trouble coming their way and he wasn't sure if they would be able to keep them at bay for long.

The former professor shook his head to clear the negative thoughts. What had already been done was done and there was nothing he could do now that would change any of it. Like Gendo, he had made his bed and now he was going to have to lay in it. As for SEELE, they would just have to find a way to deal with them.

The more immediate concern was that even though Yui was back and no matter what Gendo was planning to do they still had Angels to defeat. As much as he wanted to place his trust in the abilities of pilots Ayanami and Soryu, he knew that their best chances for survival were and had always been in the gigantic hands of Unit 01 and its reluctant pilot. But now, all bets were off. Even if Shinji would still pilot the Eva they had no idea if it would still operate now that the soul within it was no longer Yui's but Katsuragi's. Was the Major's soul even still alive inside the beast, and if it was would she be able to connect with Shinji like Yui had?

They would never know until Shinji tried to sync with it again and deep down he knew that the boy would try. He knew that as scared as Shinji was he had a great affection for his guardian and he would want to try for her sake if nothing else. He also knew that if her soul was indeed still alive within Unit 01 Misato Katsuragi would refuse to give up the fight against the Angels and she would fight to the bitter end to protect her pilot. With Unit's 00 and 02 still under repair, they would need to know soon.

"With a little luck we may all come out of this alive yet," he muttered. He sincerely hoped so.

NERV Medical

Rei Ayanami was in a state of turmoil and confusion, which was a very uncomfortable situation for the girl since she liked things to be plain, simple, and orderly. She was sitting on a bench outside of the protected hospital ward where Shinji and his mother were being kept and even her security clearance was not enough to allow her entry.

On one hand she found herself to be uncommonly pleased that Ikari had been successfully rescued from his Eva. It was what she had wanted after all. However, she felt a great sense of trepidation and foreboding at the appearance of Yui Ikari. Her life, her entire existence, had been created for the sole purpose of reuniting the Commander with his wife in a Third Impact scenario. Now that she had returned from the Eva's core, that scenario was no longer necessary and Rei feared that now, neither was she.

She may still be of some use as long as there were still Angels to be defeated, but what would become of her then? When the Angels were no more would her existence be terminated? Would she be taken into the dark recesses of Terminal Dogma and put down like an unwanted stray dog? All of the resolve and desires of what she wanted for herself as she begged Unit 01 to give Shinji back had now evaporated.

"I…do not wish to die."

She spoke so quietly that even she could barely hear her own voice. But what reason was there for her to be allowed to continue living? Soon, any usefulness that she still had to both NERV and the Commander would be at an end and she would have nothing left.

Her whole life had been structured, charted, and scheduled down to almost the last second of each day. She had no other interests outside of NERV, she had never needed any because the Commander had said it was unnecessary. She had no interaction on a social basis with others because, again, the Commander had said it was unimportant and would only distract her from her purpose. He may have told her that these things were unnecessary and unimportant, but that didn't mean that she hadn't felt a sense of isolation or hadn't heard the unkind words from those around her. Just because she gave no outward reaction it didn't mean that it hadn't pained her to even some small degree. She had simply been able to outwardly ignore it and remain the cold, emotionless puppet she was designed, conditioned, and medicated to be.

She knew full well what the medications she was required to take did to her both physically and mentally. She had been conditioned to be nearly emotionless and it had begun almost from the very moment she took her first breath. Every word spoken to her by Commander Ikari was her absolute and she had been made well aware of the consequences of disobedience and deviation. It wasn't brainwashing because there was no previously learned behaviour or thought process to subvert and change. She began as a blank slate that knew no other way and was shaped and crafted to be exactly what the Commander desired.

The mood levellers she was required to take were insurance should what little interaction she had with others cause her to waver, or even worse, evolve in her behaviour beyond required limits. They altered her moods and deadened her emotional sensitivity. More accurately they made her simply not care about whatever she was feeling. It also made her not care that she was even taking the medications. Thus far nearly all of her emotional reactions barely registered and until now had caused her little in the way of distress. The one exception to that always seemed to involve Shinji Ikari. Despite the drugs and the conditioning he seemed to be able to get through that barrier and make her feel something.

She also took medications to keep her S2 organ from being fully functional. They didn't stop its effects entirely but slowed it greatly. Enough so that it had taken ever since this second version of herself was activated to alter the human components of her DNA and mutate it to match her Angel DNA. When injured she healed more quickly, but not a fast as she could if her S2 was not constrained. Between that particular drug and the physical effects of the others, it made her feel almost numb and at times like it wasn't even real, that it and her soul weren't properly connected.

Other than to the scenario, she had no place to truly belong. She did not have a family in any sense of the word. At one time she had thought of the Commander as her family but she knew deep down that he did not care about her, only what she meant to his scenario. She was his useful tool, a means to an end with no other purpose for being. She doubted that her feelings about Shinji would even be considered in the matter. She had been created to bring the end of the world after all, not to be a normal girl with all of the things entailed in having a normal life. She had been created not to be loved and cared for, but to be used and thrown away. She was disposable.

And what of Yui Ikari? What would she think of the thing her husband had created as a conduit to reunite himself with her? Would she be repulsed by her and consider her a freak like so many others had throughout her young life? Would she desire to see her disappear?

"I am unwanted and unloved," she whispered. "I have no purpose or reason left to exist. I am no longer relevant."

She suddenly became aware of the cascade of hot tears that had began to stream down her face. A sickening, clenching feeling welled up in her chest and she felt like she might throw up. She was not used to feeling such turmoil, she had never before felt such inner pain. Having virtually no experience with such strong emotions she was left feeling helpless and overwhelmed. She didn't know what else to do, so she simply sat there, alone like she always was, and let her tears flow.

Misato's Apartment

Asuka Langley Soryu, pilot par excellence of the giant red beast known as Evangelion Unit 02, sat on the couch idly flipping through the TV channels, the remote clenched tightly in her right hand. Her face remained virtually expressionless but her mind was churning like a cauldron on full boil. He had done it to her again. The great and wonderful Invincible Shinji had saved the day once again when poor, fragile, helpless little Asuka was getting her pretty little ass handed to her.

She had looked like a complete fool, standing helpless in the Geo-front for all of NERV to see, her beloved Eva missing its arms and its head. Even that fucking doll Rei had put up a better fight. She still couldn't shake the image of Unit 00, seen on footage of the battle after she had been rescued from her damaged Eva, one arm still not regenerated from the previous battle and charging the Angel with an N2 bomb tucked under its good arm. It pissed her off to no end. She wanted to bury her fist in that bitch's face and leave her bleeding on the ground. She didn't want and she sure as hell didn't need Wondergirl's help.

She had shown nothing but scorn when Shinji was absorbed by his berserk Eva, even going so far as to place the blame squarely on him for his predicament. As far as anyone at NERV knew she hadn't been around when the last attempt had been made to free him and if she had her way no one ever would know. It wasn't like she cared what happened to that perverted idiot anyway. Or to Misato for that matter, she could fend for herself just fine. And with her out of the way, Kaji would be hers for the taking.

But she had been there and she saw what happened and she could just picture the scene at NERV. The full attention of the medical staff and all of the powers that be would be gathered around their beloved and prized idiot, making sure that he was whole and fit and ready to resume the fight. They would be falling all over themselves to help their great hero, focusing the attention of the entire organization on a useless, untrained, bumbling fool.

If he wasn't trying to run away, then he was always getting hurt. He was as unreliable as he was useless. They should be throwing their resources behind her, not him. She was the best pilot, she had the best training and an Eva that had been truly built to fight the Angels, not some test model or prototype like the idiot or the doll piloted. She would show them all how it should be done and maybe then she would finally get the recognition she should have been receiving all along.

'He just wants to be your friend. That's all he has ever wanted. He want's your friendship and he wants to help you,' a voice in her head told her. She had been hearing the voice a lot lately and she didn't like it one bit.

"I don't need that pervert's friendship or his help," she snapped. "He's useless and he's a coward!"

'But he helped you defeat the Sixth,'

"He was in the way!" she growled. "He ruined my first battle and he stole my glory!"

'He was so patient with you and trained so hard to beat the Seventh.'

"He was the one who kept screwing it up!"

'Rei synchronized with him in one try.'

"Fuck you and fuck Wondergirl! She's a lifeless doll! She's nothing!"

'He disregarded his own safety to save you in the volcano.'

"I'd rather die a warrior's death than be saved by that idiot!"

'You goaded him into taking the lead against the Twelfth.'

"It was his fault for trying to show me up! He got what he deserved!"

'You wanted Misato to punish him for being reckless.'

"She said she would! She would have punished me for the same thing but she throws herself on him and cries like her lost love has returned." She threw the remote across the room. "First she takes Kaji, now she wants the baka!"

'You kissed him.'

"I was bored and he sucked at it! Misato can have him! They can do all of the perverted things they want to each other. I. Don't. Care!"

'He saved you again from the Fourteenth.'

"After he quit!"

'But he came back and he paid the price.'

"If he wasn't so incompetent his Eva wouldn't keep going berserk!"

'His mother protects him.'

The knowledge that his mother had been within the Eva's core had brought implications to her mind that she didn't want to address and she had been avoiding thinking about it ever since she left headquarters. It was just more explosive fuel to be set off by the lit match of that annoying little voice in her head.

She flew off the couch in a screaming rage, knocking over the furniture and throwing anything she could get her hands on across the apartment. She called Shinji a useless, perverted idiot and called Misato a slovenly, drunken whore in three different languages. She called them every filthy name she could think of, insulted everything about them, and screamed how much she hated them.

'His mother protects him.'

She fell to the floor, her fists jammed tightly to her temples, her head feeling like it was exploding.

"Shut up! Shut up! Shut up! Why does he get to have his mother back?! Why him?! Why is everything always for Shinji?!"

And that, for Asuka, was the root of the matter.

Central Dogma

Ritsuko Akagi stood on a catwalk within Central Dogma, leaning on the handrail and looking down at Unit 01. Her world had just been turned upside down and inside out all at the same time. Technicians both down below and in the command centre were busy taking readings and re-calibrating equipment. In front of the Eva's core, a wide area had been cordoned off with yellow caution tape. No one was to approach it until every possible scan and reading had been taken and analyzed. Misato and Shinji's clothes were the only things within the marked off area.

Ritsuko found that she couldn't get the image of her friend's absorption out of her head. True, their relationship had been strained lately, but Misato was still her closest friend. She knew Misato was a messed up individual, who wouldn't be after witnessing Second Impact first hand, but one of the things she admired most about her purple haired friend was her ability to let her emotions show and to hell with who didn't like it. Misato's emotions were always lurking just under the surface and were easily coaxed out, while she on the other hand tended to suppress hers to a large degree.

It was so like Misato to be as upset as she was over what happened to Shinji. After all, he wasn't just her responsibility, he was family to her. It wasn't even all that surprising when she started screaming at the Evangelion and beating on its core with her fists. That was Misato Katsuragi in a nutshell. When all other options failed, she would fight, even if it meant a bare knuckles brawl against an Evangelion. Ritsuko couldn't say if she would have reacted that way if she was in Misato's place and that disturbed her a great deal. She didn't have anything in her life that she was willing to fight that hard for.

All of her life, all she had really cared about was her science, never really becoming emotionally attached to anyone or anything. Except her cats and she realized that for what it was. She had a lot in common with them, they were emotionally detached and indifferent to most of the world around them. They were her crutch, something to identify with. She let out a disgusted sigh. 'Pathetic! I have more in common with my cats than I do with other human beings.'

She hadn't fared well socially early in her life and she had been a disaster in the dating department, all of which had served to lead her deeper into her studies. It had also been one of the biggest catalysts that led her into the uncaring arms of Gendo Ikari. He had the type of personality that seemed to draw in the weak and vulnerable and demanded them to do his bidding. Even when she first realized that he didn't love her and was just using her, sometimes roughly, she couldn't walk away. Their physical relationship was the method by which he bound her to his will. She was desperate for human contact, any kind of contact, and she needed to feel loved. She didn't get that from him, but she still couldn't seem to walk away. So she settled for an illusion of love and made believe that it was real when all she really was to him was his whore.

Career wise, she had everything she could possibly want and more. She was on the cutting edge of science and technology here with NERV. Bio-mechanical technology, genetics, cloning and soul transference, the MAGI system. Any scientist in the world would sell their soul twice over to be involved with the technologies she had her hands on every day and it did give her a certain sense of superiority. A sense that she was important and worth something. A sense that was always crushed whenever she was with Gendo. Whether it was within the NERV complex or in his bed, the dominance of his personality seemed to crush her will and, over time, it had crushed her spirit as well.

And now Gendo had Yui back and in a way much better than his scenario ever could have realized. Ritsuko knew that it was the end of the line for her one sided relationship with the Commander and even though it was very hard for her to admit it, it was probably a good thing. Maybe the best thing that could happen to her. She was starting to realize some things about herself, she was seeing things happen to her personality that she really didn't like very much.

It was a rare instance of self reflection that actually surprised her but she realized that she was at a crossroads and had to make some decisions. She could either continue on as she was, thus risking what she considered to be her already questionable sanity, or she could try to move in another direction and hopefully find something that was tangible and real. Unlike her mother had, she felt no ill will towards Yui Ikari, though for a time she did resent her since she was Gendo's obsession and the only thing he truly loved. When she began to realize that she really was nothing but his tool she got over it. She had never actually met the woman and knew nothing of her other than her scientific reputation, which was considerable. However, since she saw the woman emerge from Unit 01's core she had felt a certain amount of fear.

She had no idea how much of the outside world Yui had been aware of. Was she aware of Gendo's plans and what role she had played in them? Did she have an inkling of all of the awful things that had been done? Would Yui even want anything to do with the Commander after all he had done, especially when he had abandoned and used his own son? How would she react to her, the pathetic excuse of a woman who was having sex with her husband while he schemed to reunite with her soul at the cost of the entire human race? Someone, who for all of her brilliance, was too damned stupid to get away from a man who was only using her?

"I've got a lot to answer for no matter who's asking the questions," she said quietly. "I'm such a damned fool and I'm so sick of myself. I can't live like this anymore." She offered a wistful smile to the purple behemoth before her. "I could really use your help right now Misato, and what do you do, you go and get yourself absorbed into an Eva."

She felt a vibration on the catwalk and turned to her left to see the Commander approaching her. She suddenly realized just how truly tired she really was.

"Commander," she greeted him, not bothering to move from her position, leaning on the rail.

"Doctor," he returned. "Status report."

"We're still working on our sensors and going over the readings we obtained from the event."

"I will need more than that to take to the Committee, Doctor. They will want a report on what happened, how it happened, and the viability of Unit 01."

"I'm well aware of that," she replied irritably. "Until we finish analyzing the data we won't know how or why, and we may not then. As for Unit 01's viability, that depends on whether or not Misato's soul survived the transfer. If it did, we won't know if Unit 01 will operate until we try. In order to do that we will need Shinji to try syncing with it."

"Unit 01's pilot will be made available as soon as he has been cleared from the isolation ward," he informed her coldly. "In the meantime I expect all possible measures to be taken to investigate this incident and to look into Unit 01's continued ability to operate. Are we clear on this Doctor Akagi?"

"Yes Commander, we are," she answered, barely able to control her anger. 'Unit 01's pilot? He couldn't even refer to his own son by his name, and he couldn't care less that Misato is stuck inside the core!'

"Then I expect results soon," he said as he turned to leave. "You do realize Doctor Akagi, that our private relationship is at an end." He didn't even look at her when he said it.

"Yes, I managed to figure that out all by myself," she snapped.

He simply walked away from her without another word. For her part, Ritsuko felt the sudden need to throw up.

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