Neon Genesis Evangelion: Legacy
Episode III: Revenge of Ikari

Chapter 6 – My Sorrow, Your Hope
September 17, 2004 – Gehirn HQ, Tokyo–3

Fuyutsuki sat in his office. He was crying, unable to contain his sadness anymore. He had finally come face to face with something he could not explain away. Yui had been absorbed, despite all possible precautions being taken. Fuyutsuki had activated the electronic interference devices Gendo had installed in his office, so that his pain could not be overheard and mocked by anyone listening in.

"Yui was right, SEELE was to cause for this. She was probably right about Akagi as well." Fuyutsuki shuttered. "And I let her sit at that computer and manipulate the test to trap Yui in the Core of Shogoki."

Fuyutsuki slammed his fist on his desk. "I wish I had heeded her warning a bit more seriously, I'm the cause of this. First Mari was taken, then Yui, and the reports from Berlin are saying that Kyoko's mind was broken, I should have told them both to not do the test. I've failed as their mentor, I should have given them the advice thy needed to not go forward with the test. We knew SEELE had interfered in the past, but we ignored that thinking it was safe. I thought it was safe, I was such a fool."

Fuyutsuki wiped his face with a handkerchief, and walked over the window he had overlooking the Geofront. "I knew I should have listened to Yui, she was so concerned about the other day, and I told her everything would be fine, like some sort of arrogant ass. Even if I didn't tell her to not do the experiment, I should have at least told her to fight if something happened, not just accept her fate and give in. Now she's gone, and I could have prevented it. I could've saved her from her horrific fate."

Fuyutsuki hung his head in shame. He looked over the artificial lake and saw people working in it, most likely the underwater access lanes that could be used to deeply an Evangelion to the lake. "But now I am honor bound to keep my promise to Yui and never tell Gendo it was her decision to stay with the EVA." Fuyutsuki sighed. "I also have to come up with a way to bring Mari home, but I'm not sure if it's even possible."

The phone began to ring on his desk again, and Fuyutsuki looked over at it with a pained look on his face. "Every fucking time I try to think." He said as he walked over to the incessant device. The Caller I.D. showed it was the U.N. again. Fuyutsuki wiped the sweat from his forehead with his handkerchief. "If that damn phone keeps ringing, I'm going to lose my fucking mind. I wish Ikari was here, he would at least be able to take charge of all these phone calls and shit while I worked on a solution to getting Yui, err, Mari, back." Fuyutsuki paused as the call went to voicemail as he stroked his chin. "What if I came up with a plan to get Mari back, and test it on Yui first? But what about Dr. Akagi? She would most likely interfere…"

Fuyutsuki went back to the window and looked back outside. "With Akagi around, she will constantly interfere with any plans like that. I also can't go against my word to Yui about leaving her alone or telling Gendo about Akagi either…" Fuyutsuki paused, and placed his hands on the window and leaned against it. "Unless, I can use her interference to show Gendo she caused Yui's disappearance. That way I don't have to mention my conversation with Yui, and I can still implicate her for everything she's done." Fuyutsuki said proudly. "Perfect, I just need to get her involved in the recovery attempt, to waive off any suspicion I might be onto her."

He walked over to his phone and dialed an internal extension. "Hello?" The voice on the other end said.

"Dr. Akagi, its Fuyutsuki. Drop everything you're doing and come up to my office. We have some work to do, and bring that portable computer, of yours, you'll need it."

"Yes, Deputy Director, right away." Naoko responded.

20 minutes later, Naoko arrived at Fuyutsuki's office, laptop in hand. Fuyutsuki explained what he needed her for, and she was floored.

"You want to what?" Naoko said in disbelief.

"I want to find a way to recover Yui Ikari from the Core of Shogoki. I thought I made my intention quite clear when I explained it the first time." Fuyutsuki said calmly.

"But still, I'm not sure if it's possible to do." Naoko said nervously.

"But the soul is essentially an electromagnetic field, Dr. Akagi, and that field is contained within a known space. We just need a way to isolate, extract, and contain Yui's soul, and then find some way to reform her A.T. Field into a usable body." Fuyutsuki explained.

"But… but… it's just so improbable, whatever we come up with may never work!" Naoko protested.

"I don't want to hear that, all I want to hear is that we can find a way to bring her back. Understood?" Fuyutsuki said sternly.

"Yes sir, I understand." Naoko said. 'Damn it all, they all think Yui's so great, I'll show them who the great one is.' Naoko thought.

"So, do you have any ideas, Dr. Akagi?" Fuyutsuki asked.

"Well, I guess the equipment we have should be sufficient to do the job. But I think it will require a lot of modifications."

"What kinds of modifications, Doctor?" Fuyutsuki said in an annoyed voice.

"Well, to isolate her soul, we would need to modify the ATF Detector to look for an individual signal, rather than an indication of signal strength. I'd have to focus the scanning field to accomplish that. As for isolating and extracting her soul, we would need to modify the ATF Modulators to replace Yui's soul inside of the Core to force it out. We could also use the Soul Duplication Unit and disable its coping function and simply store her inside of it until we can recover her." Naoko postulated.

"But how do we reintegrate her body?" Fuyutsuki asked.

"Well, if we set up the experiment and run the connection in reverse to run into the Link Tube, we can isolate her inside of the electrolyzed LCL, but after that it gets a bit fuzzy as to what I can do." Naoko took a deep breath and thought hard. "We could use the ATF Modulators and EMF Stabilizers to create an artificial field and force her back into corporeal form." Naoko stated.

"This all sounds good, but it seems very well thought out. Is this a contingency plan you had in place?" Fuyutsuki asked.

"It was not my contingency plan. The Berlin Branch just sent over Dr. Soryu's notes. She had set this up apparently to recover their friend who was trapped by Project Alcion. I was reading over them the other day, and they seemed feasible enough. The rough details are worked out, but I'll need to finalize them in order for it to be used on Dr. Ikari." Naoko said.

"Why didn't you mention this sooner, Akagi?" Fuyutsuki said angrily. 'She wouldn't have said anything if I didn't ask… the fucking bitch!' Fuyutsuki thought.

'Oh, shit, now I need an excuse as to why I didn't say anything sooner…' Naoko thought. "I wanted to check its viability before I said anything, I didn't want to get anyone's hopes up." Naoko said in as convincing of a voice as she could.

"Alright, then Akagi, get to work running the numbers, I want a finished plan to implement this by tomorrow, and the test set up and ready to go by the 20th. Your other projects, as of now, have been suspended until this is complete. Is that understood?"

'Good, he bought the lie.' Naoko thought happily. "Isn't that a bit of an accelerated timeline, Professor?" Naoko asked.

"You're more than capable enough if you don't have any other work to distract you from putting together this plan." Fuyutsuki said, prodding her ego. "Besides, you said you've been looking it over, you must have a solution ready to go by now."

'Great, now he's challenging my intellect, I'll show that smug son of a bitch.' Naoko thought coldly. "Yes, Deputy Director, right away." Naoko said hollowly, trying to sound as calm as possible.

"Good, now I guess it's time for you get to work." Fuyutsuki said as he motioned Naoko to leave his office. 'I hope my plan works…' Fuyutsuki thought.

"One question before I leave, Deputy Director, has there been any word on Director Ikari?" Naoko asked. "He hasn't been seen or heard from since the accident."

"No, Gehirn Security cannot seem to find him, I've been leaving him messages, but he hasn't checked them yet. With any luck we can track him down and find him before anything happens." Fuyutsuki replied.

"I hope for his sake we do find him before anything happens." Naoko said in a compassionate voice.

"So do I, Akagi, so do I." Fuyutsuki said. "Now in anticipation of his eventual return, I'd like to have a plan ready to go to recover Yui, so its time you got to work."

September 27, 2004 – Gehirn HQ, Tokyo–3

Fuyutsuki was staring at the container full of Yui's remains. It had two labels. It's previous one "LIL–SS" and a second "YUI–BM." Fuyutsuki had been staring at the container for so long, he knew every inch of it and its contents. "What have I done? I've let Yui down. I tried to recover her against her own wishes, and this is the result." Fuyutsuki said. "I thought that it would have worked, everything was set. Even if she didn't want to leave, it should have forced her out entirely."

Fuyutsuki continued looking at the contents of the container, becoming even sadder as the longer he looked at it, and then something hit him. "Akagi must have tampered with the experiment. She used the Soul Duplication System as a proxy when Yui's soul was sent directly to the Link Tube. Perhaps she did it to copy a part of her soul to result in this… in this ABOMINATION!" Fuyutsuki roared. "That fucking bitch!" He slammed his desk. "All I wanted was to bring Yui back just so I could see her one last time!" Tears were welling in his eyes as he spoke. "She didn't deserve to be taken, she deserved better than that."

He broke down and cried, as he realized why he was really upset. "I liked her, all this time, and could never accept that fact. I'm denser than Gendo for that! I just want to see her again, and tell her how I feel. I wasn't bringing her back for him, I was doing it for myself! I'm so selfish, but I don't care!"

Fuyutsuki looked back at the contents of the container. He glared at it as though it were mocking him. "I know that mess is her! I did the tests three times and confirmed it! It's her! She's in that fucking jar, and I just want her back!" Fuyutsuki screamed as he knocked a stack of stuff off his desk He noticed something that fell on top of the other stuff. It was an accordion folder of the three girls' doctoral dissertations. He picked up the folder and opened it. He spent the rest of the afternoon reading everything about their research up to that point. He read though everything Yui had to say about A.T. Fields and how they could be manipulated with the right equipment, everything Mari said about how souls can be transferred and are protected and kept inside of a physical form with an A.T. Field, and Kyoko's research on creating a body or vessel out of genetic scraps. All the research led Fuyutsuki to one conclusion, and it was something he was more than capable of doing secretly in his own lab, away from any prying eyes.

"I had the answer to everything I want right in front of me this whole time. It's astonishing sometimes how they were this intelligent without even trying. They should never have been taken from this world, but SEELE viewed them as a threat, and now I'm going to bring one of them back." Fuyutsuki said proudly.

He looked over at the container once again, no longer disgusted with its contents. "Yui, I'm going to make you a new body and then put your soul into it. I'll bring you back one way or another, I promise you that."

October 12, 2004 – Gehirn HQ, Tokyo–3

Naoko was on a mission. Someone had taken her container full of Lilith's soul and moved it somewhere. She wanted it back so she could put it into the Core of Unit–00. She found the man she was looking for.

"Fuyutsuki!" Naoko called out to him. "Can I speak to you for a moment?"

Fuyutsuki turned around to see Naoko approaching him. "Of course, Dr. Akagi. What do you need?" Fuyutsuki asked politely.

"Well, seeing as you've been missing from your office, and I've been unable to find you anywhere, I was wondering if you had any idea where a containment container may have gone. It contains the soul of Lilith, and I'd like it back so I can put that into Unit–00's Core." Naoko asked. "Didn't you use one on the remains of Dr. Ikari after the recovery attempt? Was it labeled at all?"

"Well, no, it wasn't. The indicator said to was empty and not in use." Fuyutsuki said.

"Well, can I see it? Maybe you grabbed mine by mistake and just didn't notice." Naoko said forcefully. "The indicators have a tendency to malfunction."

"I wish I could show you, but it was incinerated last week after I completed the tests on its contents, per Director Ikari's orders." Fuyutsuki replied.

"Oh, well, I hope it wasn't mine. Perhaps someone moved it elsewhere. If you do come across one lying around, please check it for the label "LIL–SS" and let me know." Naoko asked politely.

"Sure thing, Dr. Akagi." Fuyutsuki said as he walked away. "Have a good rest of your day. I really hope you find your container."

He left Naoko standing there in a stunned silence.

'Oh, shit, I did grab her container.' Fuyutsuki thought as he made his way back to his secret lab. 'I'll double check the label, but I think it does have that label she mentioned.'

As Fuyutsuki got to the lab, he entered his passcode and scanned his retina, he entered and made his way to the container with Yui's remains. He saw the labels again, and realized what he had done, there was indeed a "LIL–SS" label on the container, and partially obscured by the one Fuyutsuki had put on. 'Shit. I did grab the one she was using by mistake, which means that there's a soul in here, and it's mixed with Yui's remains.' Fuyutsuki thought. 'It also looks like I've pushed back Project E awhile. I guess that'll teach her to not secure her equipment in a safer place than a storage unit.

Fuyutsuki then looked over at a tank filled with LCL. It had a partial human figure inside of it, a torso, a bald head, left arm and the beginnings of a right arm and legs. It was the size of a small child around three or four years old.

"Ah, look at you, you're coming along nicely. Soon enough I can get you out of there and you can live a nice normal life." Fuyutsuki said to the figure in the tube. "Soon, Yui, you won't be trapped in the shadows anymore."

October 26, 2004 – Gehirn HQ, Tokyo–3

Fuyutsuki was walking into Gendo's office. He was nervous about the outcome, as he was about to tell Gendo of his secret project. He entered the office and stood a few feet from Gendo's desk. "Well, Fuyutsuki, what was so important you had to come and tell me." Gendo said calmly.

Fuyutsuki cleared his throat. "I have to talk to you about the remains of the recovery attempt." Fuyutsuki said as calmly as possible.

"What is there to talk about, Fuyutsuki?" Gendo said, his hands folded over his mouth again. "The sample was supposed to be destroyed weeks ago."

"About that…" Fuyutsuki started. "I didn't destroy it… I couldn't. I knew, even though it looked nothing like Yui, it was still her, there was something of her in that… in those remains."

"You can't know that for sure." Gendo said. "It was just an amorphous blob of tissue."

"No, it wasn't, Gendo, the DNA analysis said it was a 97.5% match to Yui!" Fuyutsuki said. "I did the test three times to be sure! What came out of that Link Tube was Yui!"

"The hell it was!" Gendo said loudly. "The Yui we both knew is gone."

"But I can bring her back…" Fuyutsuki said.

"What are you talking about?" Gendo asked. "How can you bring her back?! The recovery failed! She's been lost to the Evangelion!"

"By using their research, all three dissertations gave me a road map to bring her back from that blob." Fuyutsuki shouted back. "Those three girls gave me the key!"

"Why would you do that?" Gendo said. "Why not just leave well enough alone?"

"Gendo, this project is the personification of my sorrow, but it can also become the personification of your hope." Fuyutsuki said. "I can use what was recovered of her soul mixed with that white demon's soul."

"So you're the one that took Akagi's little canister. Well done, Fuyutsuki, you set back Project E by at least six years with that." Gendo said proudly.

"Really, by that much?" Fuyutsuki said. "I figured a year at most."

"Well, regardless of Project E, we need to finish discussing your project…" Gendo said. "So what you're saying is that you are recreating her body and putting in fragments of her soul. Will she know who she is?"

"Most likely not, copies of fragments won't do much, but she will be cognizant of everything around her." Fuyutsuki replied.

"So, it will look like Yui, but not be her…" Gendo said, trailing off.

"Most likely, and she will be a child. The material's telomeres were too new, and could only be aged so much safely." Fuyutsuki replied. "She will look around Shinji's age, three or four, and will age and mature normally."

"Then she will need a different name." Gendo said. "I'll let you complete your experiment, Fuyutsuki, Let me know when she is about to be birthed. I will be giving her a name."

"Of course, Ikari." Fuyutsuki said. "Is there anything else you wish to ask me?"

"Yes, Fuyutsuki." Gendo asked sadly. "Why did the recovery attempt have to fail? What did we do wrong?"

"I don't know, Ikari, but I'll look into it for you." Fuyutsuki said as he left Gendo's office determined to find a way to payback Naoko at all costs.

October 31, 2004 – Gehirn HQ, Tokyo–3

After months of hard work, Fuyutsuki was in the process of completing the project that had so consumed him the creation of a clone of Yui. Several days ago, Fuyutsuki had gone to Gendo's office and told him about the project. Gendo had been mad at first, but now, seeing as the clone was ready, Fuyutsuki did as he was instructed and called Gendo down to the lab before the girl was

Gendo arrived in typical fashion, sweeping into the room, his lab coat swaying behind him. "Fuyutsuki, is it already time?" He asked.

"Yes, Ikari, it is." Fuyutsuki replied. "You made it just in time by the way, I'm ready to transfer the soul into the vessel now."

"Good, I'm glad I made it just in time." Gendo said happily. "I wouldn't want to miss this. Please begin, Fuyutsuki."

"Initializing soul transfer… now." Fuyutsuki said. "Soul transfer will be completed momentarily, Ikari."

Gendo walked up to the horizontal cylinder filled with LCL. Inside was a young girl, her eyes were closed and she was covered in a hospital gown. Her hair looked as though it was light blue, and was long. It reached down past her knees and floated all around her in a big mess. But as Gendo looked at her small face, he saw someone else entirely. "Yui…" He whispered.

"Soul transfer complete." Fuyutsuki said. "All vital signs are normal, brain waves indicating everything is functioning normally."

Gendo continued to look in the cylinder at the on girl. "Understood, Fuyutsuki." Gendo said, and as he did the young girl opened her eyes. They were the bright red, and within them, he saw the kindness that Yui had in her eyes. 'Fuyutsuki was right, part of this girl is her.' Gendo thought. 'Although, it must be the LCL that is fooling my eyes, she can't have red eyes and blue hair, that's just not possible.'

The girl stirred and mouthed something that Gendo couldn't understand. She then put her small hand on the interior of the cylinder. Gendo placed his hand over hers leaving only the glass of the cylinder between them. "Fuyutsuki, can you drain the cylinder and let this girl out?" Gendo asked.

"Of course, Ikari, right away." Fuyutsuki replied, as he began the sequence to release the young girl from the cylinder.

The LCL drained and as it did, Gendo got a better look at the girl. She had extremely pale skin and her hair was in fact a pale blue, and her eyes were a brilliant crimson color. The top of the cylinder popped open as the LCL drained out. As she sat up, and was hit with oxygen for the first time she was sputtering up the LCL that had been in her lungs moments ago, and was struggling to breathe until Gendo patted her gently on the back. "Are you ok?" Gendo asked without realizing she wouldn't know how to respond.

As soon as her coughing stopped, she looked up at him with her crimson eyes and spoke softly. "I think… I… am… alright." The girl said as if unsure of what the words' meaning were.

Fuyutsuki's jaw went slack as she spoke, and Gendo was clearly shocked that she could speak, let alone put together a sentence. "You can speak?" Gendo asked in utter disbelief.

"Yes… I do not know what exactly I am saying… it just feels as though I should say it." The girl replied. "Who are you?" She asked politely.

"I am Gendo Ikari." Gendo replied.

"Who is he?" She asked, pointing at Fuyutsuki.

"He is Kozo Fuyutsuki." Gendo replied.

"So if you are Ikari… and he is Fuyutsuki… who am I?" The girl asked.

"Your name is Rei Ayanami." Gendo said kindly.

"Rei… Ayanami…?" Rei said quietly.

"Yes, your name is Rei Ayanami." Gendo repeated.

"My name is… Rei Ayanami." Rei said, gaining confidence in her ability to speak. "I am Rei Ayanami."

All Gendo could think to do was smile. "Would you like some real clothes to put on instead of that gown?"

"What are clothes?" Rei asked.

Fuyutsuki walked over and leaned down next to Gendo. "These are clothes." Fuyutsuki said as he pulled his shirt and pants. "Clothes are what people where when they are around others, for the sake of politeness and modesty."

Rei clutched Gendo's arm when Fuyutsuki talked to her. "Rei, what's wrong, why are you scared." Gendo asked.

"He is… unfamiliar." Rei whispered quietly.

Gendo wrapped his arms around the girl and turned to Fuyutsuki. "Fuyutsuki, could you go into the other room for a moment. It appears Rei has imprinted on me, and you're scaring her." Gendo said quietly.

"I understand, Ikari." Fuyutsuki said sadly. 'It figures, Yui loved him in one life, and now in this one. The universe is a cruel place.' Fuyutsuki thought as he left the room.

"Is what that man said true… about the clothes?" Rei asked.

"Yes, Rei, they are for modesty in public." Gendo said. "So, would you like some clothes?"

"Yes… I think that would be… nice." Rei said.

"Then let's get you cleaned up first." Gendo said, picking Rei up and getting her out of the cylinder. He set her on the ground and her legs were uneasy. "Can you walk?" Gendo asked.

"I think so…" Rei said as she took an uneasy step. "I will be fine…" Rei looked up at Gendo. "Could you… hold my hand?"

'She is so much like Yui, it's uncanny. But I like that she's so kind.' Gendo thought as a tear formed in his eye and it rolled down his cheek. "Sure, Rei, I can hold your hand."

Gendo guided Rei to the bathroom, where it appeared Fuyutsuki had set up a warm bath and laid out some clothes. He picked Rei up and set her into the bath. Rei yelped quietly at the heat and she took off the hospital gown. Rei was silent during the bath, and she had a pout on her face as Gendo cleaned the LCL off of her and then drained the tub and toweled Rei off. He handed Rei the clothes to put on, which she looked at puzzledly.

"What do I do with these?" Rei asked holding up a pair of underwear.

"You put them on by putting your legs through them." Gendo said.

Rei began to put them on backwards, but Gendo stopped her and turned them around. "You put them this way Rei." Gendo said gently.

Rei blushed as she put them on and almost feel over while doing so. Gendo awkwardly helped to finish dressing the newborn Rei. As Gendo helped her with her shoes, Rei, yawned loudly.

"Rei, are you tired?" Gendo asked.

"What is… tired?" Rei reciprocated.

"Tired is when you have difficulty staying awake." Gendo replied. "Your eyes feel heavy and you have trouble standing up."

"Then I believe… I am tired." Rei said, yawning again. "What does one do when they are tired?" Rei asked.

"They go to sleep, Rei." Gendo said. "Why don't I take you to bed?"

"That would be… nice." Rei said.

Gendo led Rei to another room off the lab that had a bed. He put her gently in the bed and tucked her in snuggly, leaving only her head exposed. Rei settled herself into the sheets and looked up at Gendo. "Will you be here when I wake up?" Rei asked quietly.

"Of course, Rei. I wouldn't leave you alone." Gendo said. "Now, you need to get some sleep, there's no need to be afraid, I'll be just in the other room." Gendo kissed her gently on the forehead. "Now it's time you get some sleep Rei."

"What does one say in this situation?" Rei asked.

"We say goodnight, Rei." Gendo replied.

"Goodnight Rei." Rei said.

Gendo smiled and left the room, turning out the lights as he left. He met Fuyutsuki back in the adjoining lab and walked over to him.

"Fuyutsuki, Rei is asleep. I will check on her in a few hours." Gendo said.

"Good." Fuyutsuki said gruffly.

"Is something wrong Fuyutsuki?" Gendo asked. "You seem a little… off."

Fuyutsuki sighed. "Do you want the truth?"

"It would be nice, Fuyutsuki." Gendo said sarcastically.

"I'm simply annoyed that she seems to have latched on to you." Fuyutsuki said. "And that she was so scared of me. Why was she so scared of me?"

"Fuyutsuki, she may look like a young child with the soul, but she has just been brought into this world." Gendo said. "I was the first person she saw, she has imprinted my face, so she will trust me. Give her a few weeks and she will talk to others. But I will have to look after her, and raise her."

"But why her and not Shinji?" Fuyutsuki asked. "You already have a child to look after and care for and raise, if you can look after her, you can bring him home."

"Because, Shinji is stronger than he looks, he can handle being alone. He is also well looked after by Kyoraku. Rei, the poor thing, needs to be looked after and cared for, something I could not do for my wife, or my sister…" Gendo said, trailing off to the thoughts of his lonely childhood.

'Sister, what sister?' Fuyutsuki thought as he sighed. "If you wish, Ikari, I can look after her, I wouldn't mind in the slightest."

"As I said, Fuyutsuki, she will only trust me." Gendo replied. "And I really don't mind looking after the… daughter of my wife. She is essentially my child, and my by that logic, also my responsibility."

'If only you thought that about Shinji' Fuyutsuki thought. "Ikari, why did you choose the name "Rei Ayanami" of all names?"

"If you must know, I chose the given name of Rei for my deceased twin, she was a stillborn." Gendo said. "As for the surname, I chose the maiden name of Yui's mother. It seemed to be the best choice to link Rei and her progenitor without it being so blatantly oblivious by giving her the name Ikari."

"You had a sister?" Fuyutsuki asked.

"Yes, and I do wish she had not died." Gendo said. "But the past cannot be changed. Only the future can be shaped to the way we wish it to be."

"I'm sorry, Ikari, I didn't know." Fuyutsuki said.

"Only Yui and Kyoko did." Gendo replied. "It's not something I spread around."

"Understandable." Fuyutsuki said. "Well, Ikari, if you must raise Rei, please just don't leave her alone."

"I wouldn't dream of it Fuyutsuki." Gendo said quietly. "I've had enough women in my life leave me, I don't intend to lose another one."

March 10, 2005 – Tokyo–2

It had been six months since Rei had been brought into the world. In that time, Gendo had been caring for her as a father would. He raised her by teaching her basic life skills, like how to eat and dress herself, and how to use the bathroom. Even though she looked like a young child, and was able to walk and communicate, she was essentially an infant who needed to be taught the things every infant needs to know. Gendo didn't mind doing this, as he found it quite fun.

Gendo had become far more involved with raising Rei than he ever had with Shinji, as he had left the majority of that up to Yui's capable hands. Now with her gone, and Shinji shipped off to Atsugi, Gendo had found someone to replace his old family, and that person was Rei.

During this time it was found out that due to the mild degradation of her genetic structure due to the cloning/duplication process, her stomach and digestive tract could not handle meat of any kind. This was found out after Rei tried some pork curry, and her body's reaction to it was so severe she ended up in the hospital. So her diet was to consist of vegetables and nuts, much to Rei's disappointment, because she liked how the meat tasted, but not how her body had reacted to it.

Fuyutsuki also confirmed the findings about Rei's restricted diet, and also found that Rei had a severe form of anemia, which is what caused her pale skin, and sudden tiredness. She had a severely reduced amount of red blood cells as compared to a normal child her age, which restricted what she could do for physical activities.

Rei was depressed about the news she was given, and when she asked why this had to happen with her, Gendo wouldn't let any of this bad news get Rei down, and he told her, "Rei, you are a very special girl, and these difficulties just make you more special. They make you unique." Rei smiled when she was told that and her disposition became much happier after that.

So after several months of changing diapers, potty training, dealing with medical issues, and showing Rei how to eat with utensils, and not just stick her face on the plate and eat, Gendo decided to treat Rei to day out in Tokyo–2. The reason Gendo chose Tokyo–2 was to get away from the prying eyes in Tokyo–3 and of SEELE. Tokyo–2 was the ideal place as there were far more people to blend into to avoid being tracked and watched.

Rei was dressed in a red jumper with a small straw hat to keep the sun off her face and neck. Gendo was beside her, holding her hand as they walked down the main street. Rei looked so happy, she loved going outside and feeling the sun on her face. They had already had lunch and been to the children's museum and science center, which Rei had greatly enjoyed. While they were walking towards the park, they happened upon a store dedicated to stuffed toys. Rei stopped at the window and gazed inside, her eyes wide and glassy, as though she had found her heaven and was utterly distracted from anything else around her.

"Rei do you want a stuffed toy?" Gendo asked.

Rei only nodded, still awe inspired by the sight of all the plush toys.

The two walked into the store and Rei ran around looking at every plushie she saw. Rei picked up a whole bunch of them and squeezed them to see how they felt. After about an hour of searching, Rei found the perfect one for herself. It was a small plushie of Mew which she thought looked like a cute pink cat. She grabbed the plushie and refused to let go of it, only uttering the word "Mine!" when asked to hand it over.

Gendo sighed at this, but did not care. 'She seems to really like the toy, why take it from her?' Gendo thought. 'That would be cruel.'

Next, Gendo took Rei to the park to let her run around a bit. 'Even though she'll get tired quickly, she should be able to enjoy the outdoors.' Gendo thought.

Rei happily walked beside Gendo all the way to the park, hugging her new toy. When they got to the park, Gendo found a bench to sit on while Rei ran around playing with her Mew. As she threw the toy into the air, she cried out "Papa, Look! Look how high it can go!"

After only a few minute out in the sun, Rei started to slow down. As Gendo noticed her stumble when she caught Mew from another throw in the air, he rushed over to her to see if she was ok. "Rei, are you alright?" Gendo asked.

"No papa… I'm tired again…" Rei said, quite out of breath.

"It's alright, Rei, did you at least have fun?" Gendo asked as he picked her up.

"Yes, it's nice to be outside. I like how the sun feels on my face." Rei replied happily.

Gendo sat back down on the bench after placing Rei down first. "Rei, are you sure you're alright?"

"I'm fine papa, I just don't want to leave yet. We don't see a lot of sun in the Geofront." Rei replied. "But why is it always so hot? One of the books I read said there are seasons, but the weather is always the same… always hot."

"Well, Rei, that has to do with Second Impact, it effected the weather in such a way, here in Japan it is always hot and on the verge of raining." Gendo replied.

"It's not very fun." Rei huffed and pouted. "That means I'll never see snow."

"It's not all bad, Rei." Gendo said consolingly. "One day, the weather patterns on Earth may return to their previous sate, but it will be some time before that happens, so we will just have to bare the heat for now.

"Well, I still don't like it." Rei pouted as she yawned loudly.

"Are you tired, Rei?" Gendo asked.

"No, I'm just yawning, it doesn't mean I'm tired." Rei replied precociously.

"Yes it does, Rei." Gendo said sternly. "We should be getting back."

"I don't wanna!" Rei said, crossing her arms. "I like it here, there's people and other kids."

"I know Rei, but we do need to get back." Gendo said quietly. "I know you want to stay, but we just can't. I'm sorry, sweetheart."

"If we have to go now, you'll have to carry me to the car." Rei said haughtily. "And don't forget my Mew!"

Gendo got up, gently picking up Rei and Mew, and started toward the parking lot. As he carried her to the car, he heard Rei snoring in his arms. He looked down to see a bit of drool in the corner of her mouth. When Gendo got to the car, he used his foot to open the door, and then strapped Rei into her car seat.

By the time they got back, Rei was still asleep, and Gendo brought her to her room, adjacent to his own quarters next to his office. As he kissed her gently on the forehead and quietly left the room. Gendo went out to his desk and threw himself into his chair. Gendo ran his hand through his hair. "Why do things have to be like this? Even with Rei around, I still feel like something is missing. I just want Yui back, no matter what anyone says, I know I can get her back."

"As wonderful as Rei is to have around, she isn't Yui." Gendo said sadly, spinning his chair to look out the window over the Geofront. "Just a cute little copy of her that brightens my day when I see her. But I want my Yui back, the one I'm in love with, the one that loves me, the one that Rei can never replace." Gendo rubbed his face wearily. "There just doesn't seem to be away to get Yui back. The recovery attempt proved it's impossible, I just don't want to accept the fact she is gone. I can't accept that fact, because she is down there now, trapped in the godforsaken Core!"

Gendo sighed and spun around. "I need to think of some way to be with her again." He spun his chair back around and looked at his desk. He saw the massive pile of paperwork that had stacked up from his day off. He saw a blue folder sitting at the bottom of the pile of manila folders and fished it out. "Fuyutsuki was right, I really should listen to him more. I do have hope now, with Rei, and with this folder." Gendo said. This folder will be the catalyst to bringing Yui back." Gendo said quietly. "I can finally accomplish both my goals. The Human Instrumentality Project will reunite me with my wife and foil SEELEs plans to become gods. They will feel my wrath for what they done to me. I will make them feel the pain they made me experience."

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.

Ok, so Rei was cloned using the research of Yui, Kyoko, and Mari. The reason she can talk and walk and seemingly do everything an adult can is that even though she did not gain the memories of either Lilith or Yui, she gained the genetic memory of Yui, gifting her with Yui's intelligence, knowledge base, and language skills. These are not the only things she has gained from Yui, and those will be revealed in time.

So she can speak and hold a conversation, but she still needs to be taught how to do everyday things like why clothes are important and how to put them on, and why she was having some trouble initially walking. Rei is literally an old soul in a new body. I also made mention of some real medical conditions that could cause Rei to look so pale, and also why she was constantly sick, other than just being a clone, there should be some real complications to what was done to bring her to life. Realism in fiction is fun, am I right?

Again, I know a Pokémon has shown up, and for good reason. Now I chose Mew as Rei's little toy because it is a pair with Mewtwo, making those two Pokémon related, as Shinji and Rei are related, for lack of another term, as brother and sister. However, what each one represents is different. Mew is to symbolize Yui's soul (which is partly what Rei is comprised of), and Mewtwo symbolizes Unit–01 (which Shinji will pilot). The other reason is that I really love Pokémon, and Second Impact happened well after February 27, 1996, so the games live on in this reality.

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.