Chapter 23

"Shinji believes that he's Gendo Ikari?" Commander Fuyutski asked.

"Not exactly sir," Ritsuko explained, "Shinji's DNA is unaltered, but these are Shinji's brain waves before the battle with the Angel." Ritsuko displayed two different wave charts. "And these are from after the battle with the Angel. The brain waves are completely different with zero similarities. He is Shinji Ikari, but his brain has been reprogrammed."

"How has it affected the pilot's sync ratio with Unit-01?" Fuyutski asked.

Both Ritsuko and Misato glanced at each other briefly before Misato spoke, "His sync ratio has dropped dramatically, he's barely able to meet the activation requirement."

"This is bad... Unit-01 is our strongest weapon, get the boy running the training programs, anything we can do to increase his ratio. And continue running tests on him and see if there is any way to revert him back. We can't just lock him up can we?" Fuyutski sighed, "Brief Rei on the situation and have her escort him at all times."

"Yes sir," Ritsuko and Misato said in unison and left together.

Yui who had been silent during the meeting, sat and watched the two women leave together. She was still a little rattled from having her supposedly deceased husband manifest himself through her son.

"Yui, how did this happen?" Fuyutski asked, "I thought Gendo's soul was absorbed by Unit-01? How is he free and in Shinji's body?"

"I don't know exactly," Yui replied, "But it's possible that when Shinji reached the 400% synch rate that he was in fact absorbed by Unit-01 and when Unit-01 recreated Shinji's body, Gendo took the chance to take over the body..."

"And he would leave his own son in the Eva that he's occupied for 13 years now..." Fuyutski whispered, "I hate to say this Yui, but if we cannot get Shinji out of Unit-01, we will have to continue the plans with Gendo. We're already too far in to turn back now.

"We can continue the plans for now, but Shinji's soul will not be left to rot in that machine," Yui commanded as if she expected Fuyutski to carry out the order that second. "Gendo was always meant to be the control factor and Shinji the pilot."

"To your own husband... Didn't you ever love him?"

"He was interesting, clever, devious, and I was infatuated with him at first but I've never loved him."

"Then why marry him?"

"Because he was smart, and almost as devious as I am, but since he was so madly in love with me he never noticed my own nature. And that is what made him the perfect puppet, clever enough to assist me with my own plans, but he would never suspect me of any wrong doing."

Fuyutski felt chills run down his spine. He sympathized for Shinji, for being born from this woman of all people.

"Do you think Gendo will still agree to pilot Unit-01?"

"Of course he will, he'll do anything I want him to."

"Are you still going to kill Ritsuko?"

"Not until Shinji is returned to me safely. I'm going to need her help to find out a way to get Shinji's soul back into his body."

X-X

The sun was bright and shinning through the open window, the rays of sunlight warmed his face and skin. There was a gentle cool breeze that flowed around him, sending ripples of sensation through his arms and face, and he could feel his hair being shifted around. The metal window pane was smooth, hard, and cold against the palm of his hands. All sensations that Gendo Ikari had not felt for the last 13 years. He was not allowed to leave the Geo-Front, but it still pleased him to be able to walk around on his own.

While he was enjoying all the sensations of having a body of flesh again, he looked over at his companion. She was the spitting image of Yui, besides the fact that she had blue hair and red eyes, but looking at her made him yearn for his wife. But he had not seen his wife since he had woken in the hospital room. She was probably just shocked to find out that he had finally returned to her, but this wasn't the reunion that he had been expecting.

"Which number are you?" Gendo asked her.

"I am the third Rei."

"What happened to the first two?"

"Both died during the activation test of Unit-00. After their deaths, they decided to delay my activation test until I was older."

"And what is your relationship with my son?"

"I was informed by Dr. Ikari that I am the daughter of her dead sister, making me Shinji's cousin."

"But you know what you really are right?"

"I am a clone of Dr. Ikari combined with genetic material from Lilith."

The answer Rei gave Gendo pleased him and continued walking down the hall. As he was walking he suddenly asked, "You've been looking at me with a lot of animosity, and I doubt that animosity is for my son, so it must be for me."

"I do not understand how you, as Shinji's father, would take over his own son's body. It has been my belief that parents are supposed to protect their children. Why are you here in Shinji's body?"

Shinji's face smirked at Rei, a cold and abrasive facial expression that Rei didn't know Shinji could even make, it looked odd and inappropriate coming from his face. Rei had never been unsettled by anything she had seen in the world, everything she had ever seen seemed logical and understandable, but this smirk unnerved Rei to the point that it made her joints feel cold and sent shivers down her spine. Rei quickly regained her composure, not wanting to show the slightest bit of weakness for this imposter.

"Because Shinji's body is the only one I could possess, and that's why I refused to synch with other pilots, Shinji is of my own loins, his body is compatible with my soul. And I spent the better part of the last 13 years trying to take over his conscious, but I am proud to say that my son has grown to be a strong man, I wasn't able to get the better of him once until he willingly submitted to me to save you all. Quite noble."

Rei was shocked by his response, "And now that you have Shinji's body, will you leave his soul inside Unit-01?"

Gendo started laughing, as if it was an absurd question. "I have absolutely no intention of spending the rest of eternity inside that machine. Maybe I'll give it back once this body has become old and useless."

"So you will not pilot Unit-01?"

Gendo's mood suddenly turned sour, that wasn't something that he wanted to think about. If he got into the cockpit of Unit-01, then he risked the possibility of Shinji seizing control and retaking his body. But he couldn't hope that Nerv would allow their strongest weapon against the Angels to sit around and gather dust. Yui will protect him, she could not find a way to release his soul from Unit-01, but now that he was back, she would keep him safe.

Before Gendo had time to give a response, he noticed a very pretty red-head with clear blue eyes approach him. He had already been briefed that he was not to let anyone else know that he was Gendo Ikari in Shinji's body. She became flustered when he made eye contact with her, she stopped walking, turned around, was about to walk the other way, but stopped, turned around again and continued walking towards him and Rei. Gendo thought, what a strange girl. Why is she acting like this?

"This is Asuka Langley Sorhyu, the second child, pilot of unit-02, and a love interest of Shinji's." Rei whispered.

"Does she feel the same?" Gendo asked.

"Yes, but there are certain complications keeping them apart that I do not fully understand myself," Rei replied.

Asuka approached the two of them and greeted them "Good morning Shinji, First."

"Good morning Sorhyu-san," Rei responded.

"Morning Asuka," Gendo said with an indifferent tone. Asuka's face was surprised by the cold response and started to bite her lower lip. She looked like she wanted to say something more, but was holding back.

"Ummmm... Hey Shinji..." Asuka said as she fidgeted with her hands, "Can we talk?"

"About what?" Gendo replied.

"About... You know..." Asuka was still fidgeting and looked over at Rei, "First, could I talk to Shinji alone...?"

"I cannot allow that. I was ordered by Dr. Ikari and Commander Fuyutski to escort Shinji and to not leave his side."

"Why the hell would they order that?"

"They are worried about the possible side-effects of him having synched 400% with Unit-01. He does not appear to have any side-effects at the moment, but they want me nearby in case they do arise."

"Just leave him with me for 5 minutes and I'll make sure nothing goes wrong with him. I need to talk to him..."

"I cannot allow that."

"You little... fu... aaaahhh!" Asuka screamed and stormed off. Most likely forgetting that she even wanted to talk to Shinji in the first place.

Gendo smirked at the entire exchange. "You could've just let me talk to her. I can manage to imitate my son well enough after having synced with him for so many years now."

Rei watched Asuka leave and as soon as she was out of sight, Rei turned around and got right in Shinji's face. "I will not allow you to do anything to ruin Shinji's life. He is going to come back, and you are not going to inhabit his body longer than necessary."

Gendo's smirk quickly disappeared and he gave Rei a cold stare. "We'll see about that," Gendo said coldly and started walking off, Rei followed closely behind.

X-X

Ritsuko sat back in her chair while enjoying a cigarette with a cup of coffee. She watched an image of Unit-01's schematics being scanned over and over again. She didn't know what she was looking for, but she hoped that the Magi would be able to find it. She took a puff of her cigarette, breathed it in deeply and slowly exhaled the smoke. The white smoke desperately tried to hold itself together but gradually dissipated and became nothing. Misato appeared behind Ritsuko and place a hand on her shoulder.

"What're you doing?" Misato asked.

"I'm having the Magi run a diagnostic check on Unit-01 for any discrepancies between now and when the angels started attacking," Ritsuko replied monotonously.

"Diagnostic on Unit-01? Aren't you supposed to be trying to figure out a way to make Shinji normal again?"

"There's a lot about the Evas that we don't know about. Shinji's father was the first pilot for Unit-01, but he disappeared while he was inside the Eva during the first activation test. And now, Shinji suddenly believes that he's Gendo Ikari. I don't believe in coincidences."

The Magi completed their scan of Unit-01. Ritsuko began tapping keys on the keyboard, bringing up several charts of Unit-01 when she noticed something.

"What is this?" Ritsuko asked as she stared mesmerized by the computer screen.

"What did you find?" Misato asked.

"I don't know but it's a sections of code that has become active in Unit-01 since the Angels have attacked and it's written in a strange language," Ritsuko said, "I think the Magi might be able to translate it." Ritsuko began typing more keys and got the Magi to work translating it. When the Magi finally finished translating the language and Ritsuko began to read, she was in shock at what she was reading.

"These are the instructions for Human Instrumentality."

"They were a part of Unit-01?"

"Yes, they were encoded into Unit-01. They're conditions that Unit-01 has already fulfilled and other instructions for Unit-01 to execute later down the line once the rest of the conditions are met, kind of like a computer program."

"And what happens after the instructions are carried out?"

"I don't know... But look at this..." Ritsuko continued to read the screen.

After the contract is sealed,

12 messengers will come to challenge the children of Eve,

If any messenger should bond with the first woman Lilith,

The children of Eve will forfeit their right to the throne and be absorbed by Adam,

The blood of each messenger is to be offered to Lilith,

When the 12 messengers have been offered to Lilith,

Adam will be reborn and the path to God will be open,

And the world will be remade in the vision of the Master.

"The first woman? Wasn't the first woman Eve?" Misato asked.

"No, Eve was the second woman created, the first was Lilith. But God made Lilith from the earth, the same as Adam. So when God commanded Lilith to serve and obey Adam, she refused and was banished from Eden. That is when God created Even from Adam's bone. Christianity is such a misogynist religion," Ritsuko exclaimed.

"There are even instructions on how to create Evas, and descriptions of each of the Angels. Arael, the Angel of Birds. Azrael, the Angel of Death. Tabris, the Angel of Choice and Freedom. They've known all along about the Angels attacking, and never warned us about them. Those fucking bastards..."

"Which is exactly why we can't let anyone know that we've found this. I was worried that this might happen and I had the Magi isolate this computer from the rest of the network. No one should know that we've stumbled across this."

"Agreed, but if Nerv has known all along about this contract and the Angels and Dr. Ikari is the head of the Eva Project, then that means... Oh my God..." Misato gasped.

"Yes, most likely Yui has known all along and has been manipulating everything from the beginning. Most people don't know what she's really like, but she's a cold-hearted manipulating bitch. She'll have us killed if she knows that we've found this." Ritsuko responded.

"We have to get Shinji away from her. If she is how you say she is, then it's too dangerous for Shinji to be around her."

"Slow down Misato. Think about it now, you're Nerv's Tactical Officer. We can't do that. And besides Shinji isn't Shinji anymore, he's Gendo Ikari right now."

"Fuck! Does this thing say anything more about how to change Shinji back?"

"No, it doesn't. It says that the Eva requires a soul, and only the child or parent of that soul can operate the Eva," Ritsuko replied.

"So it really is Gendo soul walking around in Shinji's body and Shinji's soul is trapped inside Unit-01..."

"Knowing this, most likely Gendo won't want to pilot Unit-01 anymore," Ritsuko said.

"No he will pilot Unit-01. He's an idiot if he thought we would just let him walk away from all of this. And when he gets inside Unit-01, then it's up to Shinji. Gendo found a way to take over Shinji's body, and Shinji will find a way to get it back."

X-X

Yui sat in her office and was examining data from when Gendo had first piloted Unit-01. She had known that since Unit-01 did not possess a soul at the time, it would absorb the first soul that it came into contact with, but she was looking through the data in hopes that she might be able to repeat the conditions for Gendo's soul to be absorbed back into Unit-01 again. The more she looked through the data though, the less confident she was that the conditions could be repeated. She decided to pour herself a glass from a bottle of scotch she kept in the back of her bottom drawer, and lit up a cigarette. She was quietly enjoying her smoke and scotch when her door suddenly opened.

Shinji's head poked its way through the door and he quietly walked in and closed the door behind him. Yui became irritated that her husband thought he could just walk-in on her as he pleased, even Shinji had the courtesy to knock before coming in.

Shinji smiled at his wife as she drank her scotch and took a puff from her cigarette and said, "I haven't seen you smoke since before you were pregnant with Shinji." He walked over to Yui's desk and pulled out a glass from her bottom drawer. Helping himself to a glass of his wife's scotch, he took a sip and started coughing hard. Shinji cleared his throat, after regaining his composure he started to laugh, "I guess Shinji's body isn't used to drinking? From what I can tell he's grown up to be an obedient mama's boy." He started laughing again and took another sip but a little more slowly and carefully.

"That is our son you're talking about," Yui replied.

"Yes, but I've just missed you so much Yui," Gendo said, "I've wanted to touch you so badly..."

Shinji's hand reached out to caress Yui's face, but Yui brushed his hand away and stood up from her seat.

"I've missed you too..." She said, and pulled Shinji close to her, "But how could you do this to our son? I've been looking for a way to get you back your body, and I was getting close but the Angels started attacking and I've been forced to focus on that."

Shinji smiled at Yui, "I knew you were trying to find a way to bring me back."

"Yes, I will get your body back, I promise you. So please don't let our son stay in Unit-01 longer than he has too. I've missed you, but please bring me back my boy..." And Yui started to weep into Shinji's shoulder.

"I'm sorry Yui... I never planned for this to be permanent, but I just wanted to see you so badly." He lifted her chin towards his face and slowly moved his face closer to hers, but Yui turned away.

"Gendo... I can't... Not while you're in Shinji's body... I'm sorry..." Yui said with tears still streaming down her face. She sniffled and took a deep breath. "I will get you your body back and when I do..." She gave him an alluring smile and hugged him tightly again. "I have some work that I still need to finish, but we can go get some dinner after I'm done."

"That would be nice," Gendo said, gave Yui a peck on the cheek and left her in the office.

Rei was waiting for Gendo when he got outside the office. He smirked to himself and made sure that doll couldn't see, it looks like his wife had become quite talented at manipulating those around her.

I believed and trusted you once, thirteen years ago but I will not be fooled again. I've planned and waited for this opportunity for so many years, and I will have my revenge Yui, Seele, and anyone who was responsible for leaving me in that machine for all these years. She actually thought I wanted my old back? I'm in a young strong teenage body again, with all the years of knowledge and experience that I gathered in my 30 years of living, before my soul was sucked up into that machine. And there's also that ripe little red-head who's in love with Shinji. When was the last time Yui and I had sex? Ohhh... I'm going to have some fun with this girl...

X-X

A/N: So this is a relatively short chapter, but it was a good way for me to get into the saddle. Sorry it took me so long to release this short little chapter, but I'm an English Major, and when you're writing 8-10 page papers for class, you don't really feel like doing any sort of writing for fun. Everyone, thanks for your patience and for the support. I think I said this last year, but I'll definitely try to be more diligent from now on.