Neon Genesis Evangelion: Legacy
Episode III: Revenge of Ikari

Chapter 10 – Death and Rebirth
March 20, 2010 – Gehirn HQ, Tokyo–3

Ritsuko's time at Gehirn had been quite interesting over the past two years. After a few months under her mother working on Project E, she was shifted to be the head of Project Alcion in the United Kingdom for further training, and for the supervision of the construction of Unit–XP.

After more than a year and half being abroad, Ritsuko was coming back home to Tokyo–3 to work once again on Project E. She was also coming back different, instead of her natural brunette hair, she had dyed her hair blonde to look different, and in her own eyes, she looked far prettier than she did.

Her VTOL arrived back in Hakone around lunch time, and waiting for her was her mother.

"Ritsuko, is that you?" Naoko said. "What happened to your hair?"

"Yes, mother, it's me." Ritsuko said. "I dyed my hair blonde, it looks cute, right?"

"Well, it just doesn't look like you anymore." Naoko replied bluntly. "I barely recognized you. I only realized it was you because you still have that mole on your lip."

"Thanks, mother, just what I wanted to hear." Ritsuko said crossly. "So, how is the MAGI System doing?" Ritsuko said, changing the subject abruptly.

"It's doing fine, Ritsuko, I've actually got the pattern transfer set up for later today." Naoko said "If you'd like to watch of course." She added hastily.

"Sure, I'd love to see your completed work, mother." Ritsuko said.

"Alright, why don't you follow me down to Central Dogma then, I can show you the computer first hand." Naoko said.

"What about my stuff?" Ritsuko asked.

"I'll have someone bring that to your living quarters, Ritsuko." Naoko replied nonchalantly. "Don't worry about a thing."

The two women then took a funicular train down below to the Geofront, where Ritsuko saw the completed Gehirn HQ for the first time. It's main pyramid and out buildings had been completed as well as the underground complexes, even though Ritsuko couldn't see them, she would soon enough.

"Wow, I can't believe the city is almost complete, but down here is spectacular. When did they finfish the below ground section?" Ritsuko exclaimed as she looked out at the complex below.

"They finished it a few months ago, and moved all available resources to completing the installation of the movable buildings and the armor plating." Naoko said.

"What about the defense system?" Ritsuko asked. "You know, the Angel Intercept System? When will that be installed?"

"Ritsuko, the AIS won't be installed until after the city has been brought online." Naoko replied. "Plus the Evangelion equipment will have to be installed first. The AIS is only to occupy the angels until the Evangelions are deployed." Naoko sighed. "Although, we're all hooping that any of these measures aren't needed."

"But what about the threat of a Third Impact from the Angels?" Ritsuko asked. "I mean they can't just assume they might never attack, otherwise they would never sink so much money, time, and resources into building the Evangelions."

"Oh, Ritsuko, it's all politics." Naoko said. "People don't realize they are being built, and in all honesty, if we didn't build them and the Angels attacked, and someone found out we didn't build something to defend ourselves, then we'd be in even more trouble. It's better to waste money on something you don't use than regret not having that something to use when you need it."

"Well, I guess that makes sense, and I guess it is better to be prepared just in case anyway." Ritsuko replied. "So how has Project E been doing anyway? What's happened with that since I was gone?"

"It's still ostensibly on hold. The Director has moved resources to finishing Tokyo–3 rather than waste time finishing the Evangelions right away. Unit–00 is still partially armored, it's only missing a lot of armor plates, but it still isn't ready for testing yet. The software still needs working out." Naoko sighed. "That and a pilot needs to be found for it and Unit–01 as well, but I'm not a part of that selection, that's up to the Director and Deputy Director."

"What about Unit–01?" Ritsuko asked. "And the Plug system? Has that been worked out yet?"

"Unfortunately, Unit–01 is still laying in a primarily unarmored state. It's restrained with heavy EM and A.T. Fields, and its armor has yet to be manufactured. That's on hold until next year I think." Naoko explained. "But its armor scheme is to be a lot different as it's a Test Type, not part of what will become the production series. That much I know for sure. The Plug System still has to be tested, and those tests are years away until we can get the software kinks out of the Evangelions themselves. Unfortunately, with all the focus moved elsewhere, there is not a lot of time to work on them. I've been told to focus on the MAGI and getting them operational, and that Project E is secondary for the time being."

"So why did you bring me back from the U.K.?" Ritsuko asked. "I didn't think I'd be needed for a while."

"Well, I wanted you to see that MAGI when they came online." Naoko said. "You should be proud of me for something. Can you fault me for that?"

'Yes, you fucking bitch, I can fault you for that. You never acted like my mother unless it suited your needs, you fucking egotistical cunt.' Ritsuko thought savagely. "Of course not, mother." Ritsuko said, hiding her true feelings. "I'm glad to see that you're life's work is almost complete. What will happen to the LAZARUS and EVE system when you've brought the MAGI online?"

"Well, LAZARUS will be relegated to basic computing somewhere on–site. EVE however still has use and will be a backup computer for Evangelion research." Naoko paused. "However, while LAZARUS and EVE are unique, the MAGI will be mass produced, and will all use a different person's personality as a template."

"Mass produced?" Ritsuko said. "Is that even possible?"

"Of course it is. Each set will be built here and then shipped with the basic software to the location they are being installed into." Naoko said. "The Personality OS won't be installed until after the system is properly installed and tested, and that would be under my supervision, after I select the candidate being utilized for the task."

"So you'll still have operational control of the other MAGI?" Ritsuko asked.

"Yes, I don't intent on letting some moron ruin my life's work." Naoko said. "That will be a cold day in hell."

The funicular train finally arrived at the station and Naoko led Ritsuko to her lab.

"Jesus, why did they design this place like a maze? It's so complicated to get around." Ritsuko exclaimed.

"I don't know, but someone clearly has a thing for wandering around aimlessly." Naoko replied. "But it's to be expected, and you'll have to get used to it if you'll, be working here."

"I know, but it's just so ridiculous. It's so inefficient to have people be lost on their way to work, what happens if there's an emergency?" Ritsuko exclaimed. "So where are we again?"

"Accidents aren't really a big concern here at Gehirn." Naoko quipped. "We're heading for Central Dogma, essentially it will be the Command and Control Center for all operations concerning the safety of the planet. It also houses the MAGI System."

The two women approached a door, and went inside after Naoko swiped her key card. The two women moved forward to look over the balcony to the platform below. There were three large servers, each were painted with white sides and a red top.

"Wow, so there are the MAGI." Ritsuko said.

"Yes, all three of the MAGI Super Computers." Naoko said proudly. "I will be transferring my personality in a few hours, and then they will be brought online."

"What did you end up naming each unit?" Ritsuko asked.

"Ah, I named them after the three wise men of the Bible. MAGI Melchior, MAGI Balthasar, and MAGI Casper." Naoko replied. "Each one will hold a different aspect of my personality. Melchior will hold the aspect of me as a scientist, Balthasar will hold the aspect of me as a mother, and Casper will hold the aspect of me as a woman."

"The perfect human dilemma to come to logical conclusions." Ritsuko said.

"Exactly." A man's voice said behind them.

The two women turned around to see Gendo Ikari standing behind them holding a young girl's hand. She had pale blue hair and eyes. Naoko recognized the hair color from somewhere but couldn't place where.

"How are you doing, Dr. Akagi." Gendo said quietly. "I didn't realize you had company, Doctor." Gendo looked at the other girl, and then realized who it was. "Ah, you're with your daughter. Ritsuko isn't it?"

Ritsuko blushed at the man's recognition. 'He remembered me…' Ritsuko thought. "Yes, uh Director. It's been a while."

"Oh, Director, I didn't realize you brought your daughter with you…" Naoko said as she thought back. "I thought you had a son though…"

"Shinji is with relatives elsewhere." Gendo said sternly as Rei stared quite blankly at Naoko and Ritsuko. "I've taken in a friend's child however, this is my ward, Rei Ayanami."

Naoko leaned forward to be at eye level with Rei, and spoke to her. "Hello there Rei–chan, how are you." Naoko said kindly to the young girl.

"I'm fine, thank you for asking." Rei replied in a sweet voice. "It's nice to meet you."

Naoko, because she was so close to Rei's face noticed a resemblance in how she spoke and looked. 'It can't be…' Naoko thought. 'She looks almost exactly like Yui, like her clone or something…'

Naoko looked visibly shaken, and Gendo noticed. 'Good, I figured you'd notice the resemblance, you stupid old bitch.' Gendo thought. 'I'm glad you look worried now, and you'll come running to me later, pathetic needy whore. And with your daughter here, I can move my plans forward again.' Gendo looked over at Rei. "Come on, Rei, let's go." Gendo said as he then turned his attention to Naoko and Ritsuko. "Well, I don't want to get in the way of your personality transfer, so we'll leave you be. Good luck, Akagi."

"Th… thank you, Director." Naoko said shakily.

As Gendo left, Ritsuko looked at her mother and saw she was visibly shaken, however, Ritsuko didn't care to know why her mother was upset, as it didn't concern her. 'I'm glad something can still make her feel an emotion.' Ritsuko thought. 'It's a shame she just couldn't feel more emotions as a mother. It probably has to do with the Director though, just because of how she is with men, it wouldn't surprise me…'

"Well, Ritsuko." Naoko said. "Let me just copy my brain wave patterns and then we can go set up the installation together."

"How long will that take?" Ritsuko asked.

"Oh, only about 15 or 20 minutes. It's not like we're moving a soul or anything." Naoko replied cheekily.

"Alright mother." Ritsuko said. "Just tell me how I can help."


Ritsuko realized she had forgotten to tell her mother something after she helped transfer her mother's thought patterns to the MAGI. Her mother told her to go settle in and then come back and help her with the final set–up in the morning.

As Ritsuko approached Central Dogma, she went inside with her new access card and realized she was a level above where the MAGI were. She was surrounded by darkness with the only light coming from the area around where MAGI Casper was situated. She went over to the balcony and looked over to see her mother down there with the director. Her eyes widened in shock and she covered her mouth to stifle the gasp she made. They didn't hear her as they were too engrossed in their conversation, which with some effort, Ritsuko was able to overhear.

"What are you talking about, Gendo?" Naoko asked. "I thought you came down before to see me, why did you have that girl with you?"

"I was simply showing her around, Naoko. She wanted to see Central Dogma, so I showed her." Gendo replied calmly.

"Why would you show a child around Central Dogma?" Naoko asked angrily. "She has no business down here."

"She does have business down here, considering she is the First Child." Gendo replied.

"She… what?!" Naoko exclaimed. "She was chosen?! To pilot what EVA?!"

"Yes, the Marduk Institute selected her several years ago, along with another child from Germany as the best potential candidates." Gendo explained. "Rei will be the pilot of Unit–00 when it is completed, while the Second Child is the designated pilot of Unit–02."

"Why my EVA, Gendo, it doesn't even have a soul yet, how will it function or sync?" Naoko said. "And when were you planning on telling me?"

"I was planning on telling you when the time came, but no that is irrelevant." Gendo said. "I came here to talk to you about the MAGI System."

"Well, the Personality OS has been installed in Melchior, Balthasar, and Casper. Each individual Super Computer's positronic brain is online. The transfer went off without a hitch, and the interconnection program and positronic network should be almost ready for activation. The full system should be coming online within the next few hours." Naoko explained. "Now is that really all you came to talk to me about?" Naoko asked.

"Not entirely, Naoko." Gendo said, stepping forward. "We may as well kill the remaining time doing something enjoyable to both of us."

Naoko pressed herself against Gendo as he pushed her against MAGI Casper. "Oh, Gendo, you want to do it right here."

"Yes, Naoko, right against the computer that behaves like you as a woman." Gendo said. "It seems most fitting." Gendo ripped open Naoko's shirt and picked her up, holding her body between himself and

Ritsuko was horrified by the sight. 'What is my mother thinking fucking her boss? Is she insane?' Ritsuko thought. 'What does he see ion her, she's just some old whore. He deserves someone far better, and less used than my mother.'

Ritsuko decided, rather than give into her own desires to sneak back out from the Command Tower and simply talk to her mother about the MAGI in the morning, and hopefully forget about the whole ordeal.

April 1, 2010 – Gehirn HQ, Tokyo–3

Naoko was walking down to Ritsuko's to surprise her for lunch. As she hadn't had much free time after bringing the MAGI online she thought it may be nice to spend a little time with her daughter and co–worker.

'I hope Ritsuko's hungry. I'd love to have lunch with her for once.' Naoko thought as she arrived at the office.

When she arrived, she saw Gendo entering the office. He left the door ajar, and the blinds on the door were open, allowing her to listen in but not be seen.

"Director, what are you doing here?" Ritsuko exclaimed.

"I came to see you. Dr. Akagi." Gendo said. "Or may I call you Ritsuko."

"You can call me whatever you like, Director Ikari." Ritsuko replied blushing slightly. "You are the boss after all."

"I am, aren't I?" Gendo said coyly. "Are you enjoying your time here so far, Ritsuko?" Gendo asked.

"Of course. I'm extremely happy here. I'm glad to have been given a chance to continue my studies while I'm working."

"What exactly are you studying, Ritsuko?" Gendo asked.

"Well I have my doctorates in Computer engineering and bioengineering already, and I should be finished with my Medical Sciences doctorate in the next few months." Ritsuko replied. "I just have to finish my dissertation and present."

"Is that what you're working on now?" Gendo asked.

"Yes, I had some free time and decided I could get some work done on it, sir." Ritsuko replied.

"You don't need to call me sir, Ritsuko." Gendo said. "I'm just trying to be friendly. Now what is your dissertation on exactly?"

"Well my dissertation is on advances in pharmacological science and it its implications in extending human life." Ritsuko said.

"Now, that is an interesting subject." Gendo said. "What practical uses could that field of study have? Would making medications to help someone seriously ill live a normal life be a part of that?"

'Why is he so interested in my work, is he interested in me?' Ritsuko thought. 'He can't be, he's with my mother, isn't he?' Ritsuko blushed a bit at the thought. "Well, yes, that would be a practical application of my research." Ritsuko replied. "Do you have someone in mind who requires treatment?" Ritsuko asked.

"No, just simply a well thought out question." Gendo replied. "Now, what about Unit–XP. I know you spent time in the United Kingdom and were in charge of the project, has it been completed yet?"

"Unfortunately it has not." Ritsuko replied. "Its main body has been completed and armored, and its mechanical to biologic joints have been installed, and right now they are working on the artificial limbs, which have been partially completed. Its left arm features some sort of claw which can be armed with a specialty auto cannon being produced, its right arm is complete, sans the massive Anti A.T. Field coated spear that will be directly attached to the arm. Its four legs have been framed out, but the process to wire, articulate, and armoring these will take several years to complete."

"Well, I'm glad that Unit–XP is coming along nicely." Gendo said. "But what about its Entry Plug System?" Gendo asked. "Has that been installed yet?"

"Unfortunately, it has not been created yet." Ritsuko replied. "We are basing its Plug System and Plugsuit off of the prototypes used for Unit–00, but because of its artificial limbs, its Plugsuit will require a lot of bypassing to allow human thought and action to synchronize with them. I was able to set up a rudimentary program to deal with that, and the team in the U.K. is working hard on it, but again, it will require time to complete."

"Well, that's more than fine." Gendo said. "It's nice to see a woman so smart and beautiful being so ready to answer any question she's asked. It certainly is nice not to hear any excuses about things being delayed."

"Delayed?" Ritsuko asked politely. "Who would make excuses about not finishing work?"

"Oh, that's not very important." Gendo said. "Whoever she is, she doesn't matter right now. All I'd like to think about is you." Gendo said, gently caressing Ritsuko's hair.

"About… me?" Ritsuko asked, taken aback by his actions. "Why would you want to think about… me?"

"Well, someone as beautiful as you deserves to be cherished." Gendo said. "Otherwise that flower will wilt, and be forgotten, and you certainly don't deserve that."

"But… I'm not that beautiful." Ritsuko sniffled. "You'd be wasting your time on me."

'God, she's so vulnerable, I almost feeling bad doing this.' Gendo thought. 'But for my plan to work, I have to do this, there's no turning back now. I guess her psych profile was right, she just wants someone's approval and affection.' Gendo now moved his hand to her cheek and gently touched it. "Now that is a true crime, a girl not thinking herself to be beautiful. I'd like to show you how beautiful you are."

"How would you show me?" Ritsuko asked.

Instead of responding, Gendo kissed her passionately on the lips, causing Ritsuko to go weak in the knees. 'Nothing like the last time someone did this, he really seems to care about me…' Ritsuko thought.

Ritsuko wrapped her arms around Gendo's neck as he picked her up and lay her gently on the floor. "Is this your first time, Ritsuko?" Ritsuko shook her head. "Well, I'll still be gentle, I wouldn't want to hurt you after all."

'He's being so gentle, why would he care, he's a man.' Ritsuko thought as she felt her heart skip a beat. 'But I feel so… happy. Why am I so conflicted about this? It just feels so right…'

Naoko looked away in shock, wanting nothing more than to rush in there and kill Gendo with her bare hands. 'That fucking bastard, he's… he's… fucking my daughter!' Naoko thought savagely. 'He's mine and that slut of a daughter of mine loves taking men away from me! I should kill her too.'

Naoko hurried away silently in a rage, not wanting to be caught spying on the two people she now hated more than anything.


Naoko was once again working in Central Dogma. It had been two weeks since the MAGI had come online, and they were still in need of minor adjustments to their programming to get everything running smoothly. She was at the control console above the MAGI towers working diligently as usual.

Naoko was also focusing heavily on her work so she could try and get a disturbing image out of her head, Gendo her lover and Ritsuko her daughter having sex in Ritsuko's office.

Unknown to Naoko, two people had walked into the Command Tower. Her daughter was cutting though the Command Tower two levels above to get to a meeting, and Rei Ayanami, who was on the same level of the Command Tower as Naoko.

Rei approached Naoko silently, and when Naoko turned around, she jumped. "Rei–chan, you can't sneak up on people like that, is not polite." Naoko said admonishingly.

"I was looking for you, Doctor." Rei said politely, simply staring at her with a blank look on her face.

"Why were you looking for me?" Naoko asked. "And how did you get in here?"

"I needed to tell you something." Rei replied. "Something important."

"Well, tell me whatever it is that is so important." Naoko said.

"Alright, old hag." Rei replied.

"What did you just say to me?" Naoko replied.

"Old hag." Rei replied, still with a blank look on her face.

"You're mumbling, Rei." Naoko said. "I couldn't hear you very well… say it again."

"Old hag." Rei replied once again.

"How dare you say that to someone!" Naoko shouted. "When I tell the Director of this, I'm sure you'll be in for a well–deserved spanking."

"But you are an old hag, aren't you?" Rei replied. "It's what he calls you, after all."

"Wha…" Naoko said. 'Why would Gendo call me that? He loves me… doesn't he?' Naoko thought frantically.

"He always says it when you're not around." Rei said. "That's what he likes to call you. That old hag is no use. That old hag is annoying. That old hag is stubborn… useless… and desperate for affection." Rei looked up at Naoko as Naoko's eyes widened in shock. "It's only fair I tell you what he says about you. I'm telling you because it's sad for you not to know."

Naoko's hands lunged at Rei's neck. "You fucking little bitch!" Rei's eyes widened in shock as Naoko's hands wrapped around her neck and she immediately began to gasp for breath.

"You little bitch, how dare you lie to me! You're just as replaceable as me!" Naoko shrieked. "He's already disposed of one child, he'll find another just like you take home and play house with! Just like he found a replacement for me!"

Ritsuko, who saw the scene unfolding in front of her cried out. "MOTHER, STOP!"


Naoko looked up as she felt Rei's neck break in her hands. She released her grip just a few moments too late and Rei's body fell limply to the floor. Naoko saw Ritsuko standing on one of the levels above her and looking down.

"MOTHER, WHAT DID YOU DO?!" Ritsuko shouted as she picked up the phone to call the Director. "DIRECTOR, MY MOTHER, SHE JUST KILLED… SHE JUST KILLED REI! SHE SNAPPED HER NECK!" Ritsuko shouted hysterically.

'What… what have I done?' Naoko thought, looking at the disgusted look on Ritsuko's face and Rei's limp body at her feet. "WHAT HAVE I DONE?!" Naoko shouted.

Naoko looked over to the MAGI and realized what she had to do. She took a few steps back and then started running towards MAGI Casper as Ritsuko shouted something. She leaped from the command tower and fell head first towards MAGI Casper. Her skull impacted and her neck snapped as she caught the edge of the Casper's casing. As she fell to the floor, she left a streak of crimson blood and pieces of grey matter and skull behind marking her body's final path to the floor. As the blood pooled around her, Gendo and Fuyutsuki ran into the room from one side and Ritsuko entered the room from the other. They looked from Rei's body and then saw her blood trail on the MAGI.

"What happened here?!" Gendo demanded. "Ritsuko!"

"It's exactly as I said happened on the phone, sir." Ritsuko said. "All I saw was Rei and my mother talking and then she strangled her. I don't know what happened to make her do that."

Gendo opened his mouth to speak but was interrupted.

"Well, I guess the reports were true after all." Fuyutsuki said before Gendo could say anything. "Your mother has been under a great deal of stress as of late, and perhaps the personality transfer had something to do with it."

"Well whatever the reason, the events here are not to leave this room, is that understood, Ritsuko?" Gendo commanded.

"Yes, sir." Ritsuko replied.

April 2, 2010 – Gehirn HQ, Tokyo–3

"Fuyutsuki." Gendo said to the man just sitting down in front of him.

"Yes Ikari?" Fuyutsuki said.

"Are the spare Rei bodies done yet?" Gendo asked.

"There are over thirty spare bodies that have been created." Fuyutsuki replied. "They are being stored in the LCL plant just above where we have Lilith stored. I have about 20 more almost ready for storage." Fuyutsuki paused. "Ikari, what do you plan on doing with all the spare bodies?"

"Well, we'll need to create a system to pilot the Evangelions remotely, they will be used primarily for that. But we will also need a spare for Rei's soul. Can you prepare one immediately." Gendo said. "But before you place her in another body, you'll have to split the soul so that part of it can inhabit Unit–00, and the remainder can inhabit Rei's new body. Her new incarnation as it were."

"Of course, Ikari." Fuyutsuki said standing up. "I'll get right on it."

"Fuyutsuki, before you go there is one more thing." Gendo said calmly.

"Yes, Ikari." Fuyutsuki said.

"In regards, to Naoko Akagi's soul." Gendo said. "She doesn't deserve to rest in peace for what she did. Not only to Rei, but to Yui and Kyoko as well. Everything she has done deserves more torture than we can give her, so trapping her within her life's work as nothing more than computer program is the best I can come up with. I want her soul removed and placed within the MAGI Super Computer using a modification of her Personality OS transfer equipment, and then we'll see how much she likes being trapped inside of a machine."

"Of course, Ikari, but I completed that task before I came up here in anticipation of what you'd ask." Fuyutsuki replied. "It was the only thing I could think to do to her soul as well. I just wish we could bring her back to life and kill her again."

"Well my plan didn't go as I'd planned for her, but the end result is the same. Naoko is dead, and Ritsuko is my eternal servant." Gendo said. "It's just unfortunate that Rei had to die to accomplish this. I want to avoid her death in the future."

"Of course, Ikari." Fuyutsuki replied. "Is there anything else?"

"That is all for now, Fuyutsuki." Gendo said. "I'll be down to see Rei reborn again, just let me know the time."

"Of course, Ikari." Fuyutsuki replied as he left the office.


Ritsuko was sitting in shock in her quarters. The events of yesterday were still playing through her mind. 'Why did my mother do that, what the hell made her choke that poor little girl?' Ritsuko thought. 'And why would she kill herself? If she really felt that guilty, why strangle Rei at all?'

While Ritsuko was still thinking, she heard a knock on her door. She went to open it and saw Gendo standing there. "Gendo, what are you doing here?" Ritsuko exclaimed.

"I came to see if you are alright, Ritsuko." Gendo said. "I also have to ask you something."

"I'm doing alright, I think, I'm still not sure what exactly happened yesterday." Ritsuko replied. "And I don't think I ever will."

"I don't think any of us will ever know why your mother did that, and tits for the best." Gendo said calmly. "Now, can I as you something?"

"Of course, Director." Ritsuko said.

"With your mother's untimely death we don't have a head of the science department or someone to oversee Project E." Gendo said nonchalantly. "I wanted to know if you wanted the job. You're the most qualified candidate we have, and I wanted to ask you before I looked for anyone else."

"But, are you sure Director?" Ritsuko asked.

"Of course. I wouldn't ask you if I wasn't." Gendo replied. "So, will you take the job, Ritsuko?"

"Yes, of course." Ritsuko replied.

"Good." Gendo said, closing the door. "Then there are a few things I need to fill you in on." Gendo sat down. "Well, as the new Chief of Project E of the Bureau of Technology's First Division, you will be privy to some highly classified items. Firstly, did your mother tell you what really happened during Second Impact?"

"Yes, she did when I started working here." Ritsuko said. 'Even though I found out from Misato by mistake when she told Kaji.' Ritsuko thought.

"Good, then secondly, seeing as you know of the First Angel, Adam, you need to know that the Second Angel, Lilith, is stored in Terminal Dogma. It was discovered here when we were excavating the Geofront shortly after Second Impact." Gendo explained.

"Wait, an Angel?" Ritsuko said, nearly falling over. "You have an Angel here?"

"We thought it being deep underground and restrained would keep it from being a danger, and that we could study it. It was, and is the best option. Officially, it is listed as destroyed, but it was a much better idea to keep it around." Gendo said. "Thirdly, do you know the true nature of the Evangelions?" Gendo asked.

"No, all I know is that they are biomechanical in nature that's all." Ritsuko said.

"Well, they are not just biomechanical, they are clones of the Angels, Unit–00 and Unit–02 are based on Adam, while Unit–01 is based on Lilith. There are far more intricate details we need to go over about them, such as how a pilot can sync with them, but that can wait till later." Gendo said. "Is all this making sense to you, Ritsuko?"

"Yes, it's just a lot to process all at once, even for me." Ritsuko said.

"Alright, lastly, this piece of information was unknown to your mother, but it is pertinent that you learn about it anyway." Gendo said.

"I find it hard to believe my mother didn't know something." Ritsuko said.

"Well, in this case she didn't." Gendo said. "Rei's true nature was not revealed to her at the time, nor was it ever supposed to be. This is the most highly classified piece of information we have here at Gehirn, and you, under any circumstances, are allowed to tell anyone about what I'm going to tell you."

"Alright…" Ritsuko said nervously.

"Rei is a clone of my wife and Lilith. After the experiment my wife did failed, Fuyutsuki tried to bring her back, and the result was Rei. She can't die, as there are spare bodies for her to take. It's a lot to explain, but I want you to know that she will be you primary concern, as you will be her physician when she is reborn. That's the reason you can't tell anyone about her death, otherwise Rei would never be able to be seen again."

"Understood, sir." Ritsuko replied, in utter shock at what Gendo had just told her.

"Now, even though this is a lot, there is still more to go over. But that can wait for now, as I want to comfort you in the best way I know how." Gendo said seductively.

Ritsuko without even hesitating, took off her shirt. "I wouldn't mind the comfort you're offering me at all, Gendo." Ritsuko replied just as seductively as her lover.


"You're late, Ikari." Fuyutsuki said admonishingly to Gendo as he arrived. "The soul transfer to Unit–00 is complete and I'm about to finish the transfer to Rei II."

"I was busy, Fuyutsuki." Gendo said. "I was telling Dr. Akagi of her new position here at Gehirn, and some of the classified information she needs to be privy to now."

"So, you told her about Rei…" Fuyutsuki said glancing over at the shell that would become Rei II in short order.

"Yes, I thought she may become hysterical if she saw a dead girl walking around. I thought it best to fix that problem before it was created." Gendo said. "Are you ready, Fuyutsuki?"

"Yes, the final checks have been completed, initiating soul transfer, and body resuscitation." Fuyutsuki replied, tapping several keys on the command console in front of him. "Operation, complete."

Rei's crimson eyes opened again inside of a tank of LCL, she looked around and saw Fuyutsuki and Gendo standing there. Gendo saw she was awake and walked over to her. "Rei, are you alright?" Gendo asked kindly.

Rei simply nodded. She felt odd, her neck tingled like something had happened to it, but she couldn't quite remember what, she didn't know what day it was and felt confused as to why she was in the lab. Perhaps I was taken ill…' Rei thought.

Gendo, seeing that she was alright, drained the tank of LCL and let Rei out onto her very unsteady feet.

"Rei, are you sure you're alright." Gendo asked her again as he helped steady her.

"Of course, papa, I aam fine." Rei replied. "I am just confused as to why I was in there. Did something happen to me?"

April 4, 2010 – Undisclosed Location

The twelve monoliths lit up in a flurry of light, and the men behind the monoliths began speaking immediately.

"Gentleman, calm yourselves, there is no need to panic." 'SEELE 01' implored.

"You've got to be kidding!" 'SEELE 05' shouted. "A very important ally of ours is dead and there is no cause for concern."

"I want to know exactly what happened!" 'SEELE 04' demanded. "How does the head of the research department commit suicide? Was no one watching her?"

"The woman was mentally unstable, according to her own psychological profile." 'SEELE 01' said calmly. "Apparently with the massive workload she had and the even more massive delays she had on the MAGI and Project E, she was "stressed beyond measure" as Dr. Shikinami puts it in her report. And that psychological evaluation was from two years ago, who knows how much worse Akagi has gotten since then."

"How is it possible to not have evaluated her in over two years?" 'SEELE 07' demanded. "Did she avoid the psychiatrists by hiding away?"

"She claimed she was too busy to take time away from her loaded schedule." 'SEELE 02' said. "We brought this on ourselves by putting so much on such a brilliant fragile mind."

"Who will take over for her?" 'SEELE 09' asked. "We can't go without a research head for too long, our plans have already been severely delayed."

"Ikari has offered the job to Akagi's daughter." 'SEELE 01' said. "She has gladly accepted it. She has a similar set of vulnerabilities as her mother, but according to her psychological profile, she wishes to surpass her mother, meaning she won't want to end up dead like her, she's a fine choice."

"So, Ikari goes off and makes another unilateral decision." 'SEELE 11' said sarcastically.

"He is the one in charge of Gehirn, and he is one who ultimately makes a final decision for staffing based on our recommendations." 'SEELE 03' replied. "We cannot question his every move. Clearly he trusts Akagi's daughter, and if the stories are true, she is just as intelligent and capable as her mother, meaning she is an asset to our goal of instrumentality."

"Fine, but now that Akagi is dead, and a replacement has been found, how do we distance ourselves and Gehirn from this incident?" 'SEELE 10' asked.

"Quite simply, gentleman." 'SEELE 01' replied. "We enact the name change plan we came up with years ago. I have already given Ikari instruction to change everything over, making Gehirn a more military organization to prepare for its coming mission, destroying the Angels."

"So it will be renamed then?" 'SEELE 08' said. "How simple, changing the name will make the people forget and distract from the incident, brilliant."

"Well, seeing as your fears of this incident exposing us have been assuaged, that should be it for this evening." 'SEELE 02' said.

"Not quite." 'SEELE 04' said sternly. "We have to discuss two other individuals. The survivor of Second Impact and that damn spy the Chairman decided we needed to look after Ikari."

"The spy is needed!" 'SELLE 05' shouted. "Ikari cannot be trusted, he gives us useful information on Ikari's movements!"

"So, do we really need a spy near Ikari that he can turn?" 'SEELE 10' shouted back.

"Yes, the rewards of learning about Ikari far outweigh the risks of Agent Kaji being turned against us." 'SEELE 01' said authoritatively. "We pay him quite well, and we have moved him up the ranks in Gehirn to make sure he is given a large amount of autonomy. He is the perfect agent. No one would suspect him of being in our pocket, and I know Ikari is completely in the dark about his true task."

"Fine, he may be essential, but why hire the survivor of Second Impact? Isn't her post traumatic stress going to hamper her ability to be effective in the structure of Gehirn?" 'SEELE 12' demanded. "Who made that decision, Ikari?"

"Ikari decided to hire Ms. Katsuragi because she wanted to keep a Third Impact from happening, and at the Core for Gehirn and its successor, the public image of preventing Third Impact is very powerful and will give us many people who wish to help." 'SEELE 01' said sarcastically. "And the best part is they don't even realize they are bringing about the end of the world as they know it and delivering it right into our hands." 'SEELE 01' paused. "She is the best choice to have around, as anyone who finds out about her past will never question her motives and will give us added security from someone finding out about our true goals. We need to give her a position of high power when the Angels attack."

"Why not give her operation command of the Evangelions?" 'SEELE 02' suggested. "That would give her the revenge she seeks on the beings that killed her father."

"Excellent." 'SEELE 01' said. "Now that her role has been taken care of, is there anything else, or can we end this meeting and go about our daily routines." 'SEELE 01' paused and listened for more comments. "Good, now that this is settled, consider this meeting closed."

At this the monoliths went dark again, looking even more ominous than they did while activated.

Keel Lorenz got himself out of his chair and limped around to leave his secreted room.

"Good, now things can start to pick up again." Keel said. "I can't wait to take over the world through instrumentality, even if I must modify my body to keep me alive till that day, I will take the world in my grasp and become a god!"

April 7, 2010 – Gehirn HQ, Geofront–01, Tokyo–3

Rei was sleeping in her new room deep within Gehirn HQ. Her eyes were fluttering around wildly underneath her eyelids, she was shaking, and had begun to look paler than usual. Rei woke up with a scream clutching her neck. Rei was breathing heavily and just sat there sitting up in bed.

'Why do I keep having these nightmares?' Rei thought. 'The last five nights have been the same, I feel myself being choked and my neck snapping and then I wake up almost unable to breathe.' Rei thought as she felt her neck. 'It feels like a memory that I just want to forget, but it will not go away, like its forcing its self on me. I need to ask papa about why I feel these things while I'm asleep, and maybe he has something to make the nightmares go away.'

Rei's breathing started to sound less ragged, and the phantom pain in her neck started to subside, she decided to lay back down and go to sleep, but instead she fell back into a nightmare she just couldn't escape, and this time, it was the clearest it had been.


"He always says it when you're not around." Rei said. "That's what he likes to call you. That old hag is no use. That old hag is annoying. That old hag is stubborn… useless… and desperate for affection." Rei looked up at Naoko as Naoko's eyes widened in shock. "It's only fair I tell you what he says about you. I'm telling you because it's sad for you not to know."

Naoko's hands lunged at Rei's neck. "You fucking little bitch!" Rei's eyes widened in shock as Naoko's hands wrapped around her neck and she immediately began to gasp for breath.

"You little bitch, how dare you lie to me! You're just as replaceable as me!" Naoko shrieked. "He's already disposed of one child, he'll find another just like you take home and play house with! Just like he found a replacement for me!"

Ritsuko, who saw the scene unfolding in front of her cried out. "MOTHER, STOP!"


End Flashback

Rei screamed in agony again, grabbing her neck and then throwing up all over the floor, finally remembering what happened. Rei wiped her mouth and started crying. 'Why did that happen? I was dead, how am I still alive?' Rei thought as she felt her neck again. 'My neck snapped from Dr. Akagi choking me, I should not be alive, I should be dead.'

Rei looked around her room and realized the reason she was down there. 'Papa does not want me anymore, because I'm not me anymore. I may be Rei Ayanami and have all of her memories, but I am not the little girl he fell in love with…' Rei thought. 'Because Akagi killed me, he doesn't see me as the same Rei anymore…'

Rei laid back down and still kept feeling her neck. 'Well, I'll prove to papa I'm no different than the other Rei.' Rei paused and reached for the Mew plushie sitting on the shelf above her head. 'I shouldn't call him papa though… I need to call him Director Ikari… Director Ikari was the other Rei's papa… to me he is not a father, just a man I remember… I am not the first Rei, I am the second… and I need to gain his approval again, because he means something to me…'

"I guess I really am replaceable…" Rei said as she wept silently till she fell into an uneasy sleep holding the Mew plushie tightly against her chest.

April 8, 2010 – NERV HQ

"Ah, Fuyutsuki, welcome." Gendo said. "How are you today?"

"No different than any other day since Second Impact, Ikari, worried about the future of mankind." Fuyutsuki replied.

"Well, I have some good news then." Gendo said in an uncharacteristically happy tone.

"What is this so called good news?" Fuyutsuki asked.

"Fuyutsuki." Gendo said. "Effective today, all signage in this complex is to be updated."

"To what, Ikari?" Fuyutsuki asked. "And how is more work in addition to what we have to do deemed good news."

"To read NERV, Fuyutsuki." Gendo said, a smile crossing his face as he said it. "Our plan is finally moving forward. With this new name comes new responsibilities. We are being reformed into a paramilitary agency to fulfill our mission of stopping the Angels and preventing Third Impact. We get new titles to reflect this, Sub–Commander Fuyutsuki."

"Sub–Commander?" Fuyutsuki asked.

"Yes, Sub–Commander." Gendo said. "I have been made NERV's Commander, we will have a tactical division with a rank structure similar to that of the military, and the scientific division will be comprised of mostly civilians and supplemented with our own personnel. The construction division and the technical division will be comprised mostly of the enlisted ranks. And Section 2, our intelligence division will be comprised of only officers."

"So, what operation authority do we have?"

"When the Angels are set loose, we will be able to override the U.N. and JSSDF forces and be given operational command of any situation dealing with the Angels." Gendo replied.

"So, Commander, do we need a press statement?" Fuyutsuki asked. "Any statement of the change."

"Something small, Fuyutsuki." Gendo replied. "This name change is to cover up the death of Dr. Akagi and keep it from being splattered over the front page."

"What about the signage?" Fuyutsuki said. "What should it read?"

"Ah, I drew up an emblem several years ago when SEELE suggested a transition to a new name and purpose, and using Akagi's death to force the change is in our favor."

Fuyutsuki took the emblem and looked at it and frowned. "Are you sure about the motto for the agency, Ikari? I mean Gehirn's was "For the Betterment of Mankind," but this, isn't it a bit pretentious?"

"Not at Fuyutsuki, when the Angels are known to the public and begin attacking, what better motto to have? What better way to describe ourselves than with this this motto." Gendo said slyly. "For if God's in his heaven, all's right with the world."

To Be Continued

A/N: I do not own Evangelion or any of the characters, GAINAX and the other distributors of NGE related material do. I am simply using them as a backdrop for my fanfic.

Well, if you don't know where I got the name for this chapter, I'd have to ask if you've been under a rock, Patrick Star.

Yes, I am a fan of Death & Rebirth, as it remastered Rei's smile from the show into something that had a budget behind it, and yes, it does contain the opening 30ish minutes of EoE, including that scene with the thing in the hospital, and is a glorified clip show (of some things that didn't actually happen in the show), but I still find it enjoyable. Now the chapter title not only references the change from Rei I to Rei II, but also the death of Gehirn and the birth of NERV, and also Ritsuko taking her mother's place, both as the lead scientist for NERV, but also as Gendo's new lover.

This was a hard chapter to write mostly for the death of Rei, as it was not something I was looking forward to (almost as much as her transition to Rei III will not be fun to write either. And yes, in my story Rei remembers how she died, and her soul is split to go into not only her new body, but also her own Evangelion, Unit–00

Now, I made a good explanation as to why the MAGI at NERV HQ were able to resist hacking by five other MAGI Systems from around the world, and why the computer denied Ritsuko's request to self–destruct (which was denied by her Naoko as a woman). By having Gendo throw Naoko's soul into her pride and joy, he shows her what it's like to be trapped inside of something she helped create, essentially she has become her life's work. Now, on its face, five MAGI vs. one MAGI should be no contest, but if the computer didn't just have an imprint of her consciousness, but actually have her soul, then it would explain its ability to work more efficiently in stopping a massive cyber–attack from SEELE, and also why the super computer is viewed as so unique, even though there are others in existence. Now, each aspect of her soul split apart on its own, going to its rightful place in each of the three MAGI.

Now as I said in Chapter 8, Gendo's plan was never for Rei to get killed by Naoko, however, some plans do tend to go awry, as after Naoko saw Gendo seducing her daughter, she was already at her wits end, and then Rei came and threw down her line, as a child generally would and Naoko snapped, and decided to take revenge, then, feeling guilt for what she just did to the man she still loves, throws herself onto MAGI Casper instead of facing Gendo and his rejection and her own wrongdoings.

As I said before, and will always say at the end of chapter, please leave comments, as I would like to try to improve the story going forward any way I can. And, hell, constructive criticism is a good thing.