Author's Notes:

I plan on using Eva canon for the most part. However, there are and always will be some key issues that never sat well with me regarding the use of religious imagery. It bugs me that the creators took so many cool religious elements and made them into a separate mythos for the show. Perhaps I am showing a little bias because I am from a Judeao-Christian background, but such things as making the Lancea Longinus a weapon of massive scale without some back up story really bugged me. I'll try to address some of that as I come to it. As well as other questions, like how did they manage to get the berserk Eva back into the cage after eating the Angel, when in the episode before the Nerv staff was concerned because they could no longer control said Eva. I always thought that was a poor transition and very anticlimactic. I'll see if I can do anything satisfactory with such story elements.

Some of the characters are going to be noticeably OOC. I feel when you substitute such a key figure as Gendo Ikari and replace him with Yui, the ripple is dramatic and noticeable. Some characters may be present that weren't, and vice versa. Some characters may be altered to the point that they are barely noticeable. I feel for this sort of fic, this is called for. Still, it will probably leave your average purist feeling ill. I ask that when weighing whether a character is suitable or not, contemplate the context of the story. If I have still screwed up, let me know.

Disclaimer- You people know I don't own evangelion or anything else. I mean come on, who sues fanfic writers anyway.

Prelude

2004

Fuyutsuki turned the key on the apartment door. He was in the middle of pushing the door open when he hesitated to cherish the breeze that rolled across the porch. There were few things that could offset a summer day like a cool breeze. Since Second Impact every day was hot. It made the air flowing in front of his apartment golden.

Kozo smiled, and finished opening the door. He took his suitcase to the table while pulling the collar of his shirt loose. He picked up the remote for the television on his way back to the living room, and turned on the news.

That was when Kozo caught a glimmer out of the side of his eye. He turned to find Gendo Rokubungi (Gendo Ikari he amended in his mind.) The man was pushing his glasses up on his face. He had taken to wearing a new pair recently, and they were apparently oversized. He was around a corner of the apartment away from the entrance room, so Kozo had been blind to his presence until now.

Gendo had worked his way into Kozo's life and changed its direction entirely. Kozo was still never sure if he was grateful or displeased with that turn of events, though most of the time he leaned toward the latter. Gendo had a face full of rough beard growth that Kozo still felt needed perpetually slapped, even after he had come to understand some of what the man was about. Of course, Kozo was not so doddering that he couldn't recognize a bias on his own part. He had to admit that Gendo held himself admirably in the murky waters that were Seele's will. He was driven and cunning, and willing to do what it would take to make the job happen.

This was why the gun that was trained on Kozo in Gendo's hand was all the more menacing. Kozo stood frozen, unable to think of what to do next.

"I suppose I should look into better security," Fuyutsuki finally blurted out as nonchalantly as he could. Perhaps if he could pretend to be calm, he could become so. As it was, his brain was locked with fear and the desire to run. He barely kept himself under control.

Gendo smiled as he brought his hand back down from where it had pushed up his glasses. He reached to the table, and pressed a button on a hand-held player. Slowly Kozo heard a conversation that consisted of his voice, Yui Ikari's, and her two-year-old son's frequent laughter and childish interruptions. It played for a minute, and Kozo's face went pale as he realized the particulars of the dialogue. He started to speak, and Gendo merely pointed the gun with a bit more determination at Kozo. So he waited for Gendo to turn the machine off.

"Many men would already be angry with another who would frequently go off with their wife unattended. Imagine how much more that anger would be if he discovered that the two are plotting said wife's death."

Kozo sighed, and turned to look at the wall. When given such a bold statement, it was hard for him to meet Gendo's eyes. "Not death, Ikari. It's a means of subverting Seele's plan to a desired outcome." Kozo looked at the table where another device was sitting. It resembled a trio of speakers, and a red light was flashing on top of it.

Gendo followed his gaze. "This is an anti-surveillance device. We can speak freely here. I swept your apartment for bugs, as well as yourself before I planted my own." There was a hint of a smile. "You remember me dropping my pen yesterday?"

Kozo suddenly did, and remembered the way Gendo had picked it up had seemed odd. Gendo went on, "This is all incidental. How is trapping my wife within a golem going to subvert Seele's plans?"

Kozo did manage to meet the man's eyes briefly then, before finding some other place for them to be. "She wants to do it… for Shinji. According to the prophecies, only a woman's soul can fuse with Eva. And according to the prophecies…"

"Ah yes, the Dead Sea Scrolls. Tell me Professor, after what you've seen us do, after 'Antarctica', could you believe that a prophecy is anything as limiting as a literal account of what can or cannot be? There are passages that are open to interpretation, and those that are closed to them. Our plans are merely as simple as extracting various possibilities to a given metaphor in a scripture. And yet you could not conceive of such a way of doing this that would not destroy my wife."

Kozo's eyes flashed anger. "It's not as if you love her, Rokubungi! Yui was just a way for you to worm into Gehirn and Seele! This marriage, this family, this love you've inspired in her is just a farce for your manipulative goals." Kozo realized he had said too much, and the cold metal that he suddenly felt on his temple was a suitable exclamation point to that notion. Gendo had moved fast. Murderously fast.

Through gritted teeth Gendo addressed him, "Good, Professor. Let's be frank. I tire of us walking on eggshells around one another. You've always wanted my wife. She's sweet, she's brilliant, and she respected and admired you. What's ten years age difference really? So what if she was a student? You hate me because you are not me, Professor Fuyutsuki."

"That's not…" Kozo started, before the gun being pushed between his eyes interrupted him.

"If I can hear the truth, so can you, Professor."

There was a pregnant pause, but neither man seemed inclined to say more. Gendo settled back into his chair in the corner. "You were correct up to a point. I was using Yui. You see, I have never had to adjust my actions to choose between my wife and my goals. This is the dilemma Yui and yourself have brought me."

"So do you plan on stopping her?"

Gendo placed the gun on the table. "Indeed. I plan on replacing her."

Kozo's face turned to a dark. A suspicion immediately crossed his mind. "Naoko?" It was impossible for anyone not to notice the regard that the woman gave Gendo, and he did a good job of deflecting obvious flirtations while not rejecting the woman. Yui had said when she confronted Gendo about this, he had pointed out that the creator and expert of the Magi system was not someone their team needed as a woman scorned. It hadn't sat well with her, but like so many things Gendo did, it was analytically sensible.

Gendo laughed. "Clarification is required. I plan on taking her place."

Kozo's thoughts raced. Was such a thing possible? "You can't. The gender use in the scripture is very specific. And Yui would never allow it."

Gendo pat the playback device at the table, which was in front of the surveillance countermeasure device. "I have been creative with this recording. I've dubbed the conversation so that it would call Yui's sanity and self-preservation into question. Especially since she makes so many remarks concerning Shinji coming closer to her through her demise. Don't worry; I've edited out your inclusion in the conversation, as well as anything that would send up red flags if this were to fall under the committee's scrutiny."

"I could never have Yui committed Gendo…"

"After I have gone into the Prototype, you won't need to keep her in an institute. A battery of tests will reveal my wife to be sane. In the midst of a conspiracy to destroy mankind, she is still among the least paranoid people I know." Gendo smiled. "I'll be effectively out of the picture, and you will be the obvious source for consolation."

"You do not give me enough credit, Gendo. I would never…"

"Save it, Professor. You have done an admirable job of relegating yourself to the position of a doting father figure. But there is nothing as acute as a husband's jealous regard for detecting the longing looks of other men for what he has."

Kozo tried a different tact. "There is a reason for Yui to be the one to go into Eva. You are a conniver and manipulator, Gendo. Our present conversation is testimony enough for that. If we are to create our own scenario, we might only succeed under your guidance."

Gendo smiled. "Nonsense, Professor. Yui and yourself can learn how to carry a poker face, and my wife is more than intelligent enough to outwit the committee. I will leave you with one plan, and that is all I can do. You have the prophecies to guide you. There will be no problems that will prove insurmountable. If there is one thing that the predictions dictate, it is that we will somehow defeat the Angels when they come, save the final enemy. And that is merely dramatically vague."

Kozo looked at Gendo hard for a moment. His eyes flickered to the gun, and then back. "Why?" he finally managed.

Gendo pointed to the table. "I have listened to that recording many times since yesterday. I have tried to imagine going on without Yui, and cannot. She is the only person I've known who has truly known me, and not been frightened away. I did not know how much that meant to me until the possibility of living without it arose. As for Yui, she loves me, but her love for Shinji is a mother's love that far outweighs anything else. I think it may have been all she's ever wanted. She'll go on in my absence if she still has Shinji. I'm not sure I can say the same."

They were both silent for a while. Kozo was the first to speak back up. "Contemplating this whole situation leaves me feeling dirty."

"Indeed. For me, leaving the South Pole to let half of humanity die drove home the fact that life is full of moral quandaries."

Kozo nodded. "There's still the problem of gender. The text is pretty specific."

"The actual word translates into mother or progenitor, professor. And let's just say I have an ace up my sleeve for that problem. The golem will recognize me as an appropriate soul."

Kozo contemplated this. "Castration?"

A slight smile spread across Gendo's face. "A solution both painful and irrelevant. Besides, I have a sample from Lillith that should prove less emasculating."

Kozo's eyes widened at that. Gendo really had gotten into the thick of things. Could they afford to loose such shrewdness to the role of a pilot enhancer that wouldn't even see use for another decade?

Fuyutsuki's thoughts drifted back to Yui. Though he tried to cover his heart's desire with denials and noble intentions, the outcome of his ponderings went a predictable course.

"What do I need to do?"

Gendo let his gun rest in his lap. "Stay out of the way, Professor. You have the resources to stop any of this. Don't. When I have carried out what I have planned, you may see to it that Yui is released. Tell her what I did, and that I did it… for Shinji. He needs a mother to care for him more than he needs her as a piloting aid."

Kozo was disgusted for a moment. It was a bold and shameless lie. But it was hard to keep any righteous indignation for such a small falsehood when he was betraying Yui's trust. He looked up as Gendo laid a manila folder on the table. "Burn that when you are done." Gendo packed his electronic equipment and handgun into a duffle bag that had been under his seat, and made his way to the door. He turned back to Fuyutsuki. "You are the kind of man I thought you would be, Professor. Maintain such character in my absence."

And then he was gone.

Kozo walked over to the folder and opened it. The first words were enough to catch his breath, and he read and reread the document for most of the night. He could not sleep, and his mind drifted back over the contingencies and dynamics of the ruthless proposal of Gendo's 'Human Instrumentality Project.'

A week later

The clinical smell and white rooms were almost a thing of the past, and Yui was anxious to be out of this place. It felt like a small eternity since she had seen Shinji, and the worry was wearing on her. She thought it would not have been much longer before the tests and evaluations of her sanity might start coming up with results. Her stomach fluttered, and her step was lighter. The idea of seeing her son was enough to overshadow the trepidation she felt at confronting Gendo.

Yui had been informed that it was Gendo that had her committed to a psychiatric evaluation. He had provided some proof that called her lucidity into question. She knew her husband well enough to know what a small matter it would be for him to manufacture such evidence. Still, this level of betrayal, towards her… and at this juncture in their plans. There was something else to it. It would not save Gendo from her wrath though. She had been given a lot of time to ponder these last few days. If Gendo and her fell out, how would that fare for all of mankind? Did she need to risk humanity because she had an insane husband? Was this because he was trying to stop the tests with Unit-01? Or was this a stunt for him to get closer to Seele at her expense? Through her ponderings she had to hold to one thing: she was sure her husband loved her. The only thing she could do now was confront him with the situation.

Professor Fuyutsuki was the one who was waiting for her in the lobby. When she went to speak, he shook his head, and turned to get the door for her. Confused, and now scared, she went out of the building, and walked with him to his car. Her fear mounted with every step. Her attempts to talk were shushed again until they were safely within the confines of the vehicle.

"I can't take this professor. What is going on? Where's Shinji? Where's Gendo?"

"Shinji is safe. Gendo is… gone."

Yui looked ready to cry. "What?"

"Into Eva."

And then the tears flowed.