I would first like to apologize for some of the past chapters. They escaped from me and found their ways onto the Internet before I could double check spelling and grammar. I will also be increasing the speed at which they are released. Secondly, I tried to answer some of the reader's questions. Thank you Narsil750 and Iron Duke for pointing out a number of of the little bugs and errors in the plot, I hope this chapter clears them up. Thank you kindly for your comments; they are truly what keep me going. That and that fact that this remake is nothing more than an onramp for its own sequel. I live, I breathe, I sync, and I die. Which will be released after the end of this story, but don't worry, this one's is just hitting the halfway mark. I hope you enjoy,

Kristopher

His Decision,

Her Decision

I'm not my father. Shinji thought to himself sadly, his eyes watery and his mall 'purchased' new advanced SDAT playing at full blast. That's why we're no longer together. We should have never gone to NERV! I should have never gotten jealous of her and my father, Shinji continued to think to himself. It was not my intention, it's just the only time I truly felt good is when he congratulated me on my kill of the Angel, I loved getting his attention and his praise, and Rei got it without even trying. That was why Shinji was really jealous, and perhaps why he slightly missed his father…he missed the praise. Hearing 'good job' from Misato didn't make him feel good, even though she loved him like a son, why did it feel so good for a man who treated him like shit to congratulate him? He hated his father, and yet, still strived for his acceptance…Shinji was indeed only fourteen, he didn't truly understand his reasoning for all his actions, he just followed what he believed to be true. And the hate/affection feelings he had toward his father were just another immature emotion he wanted to grow out of. But now he had Rei! She was amazing…well he did have Rei, and after she was on his computer and it must have reminded her of how much she loved her Commander. The young boy reached up and felt his cheek, the same place where Rei had slapped him all those months ago, when they had just met, and when he had spoken ill of his father. His let his eyes and head fall to the side as he lay on his bed, he was again tired and it became increasingly hard to keep his eyes open, but when they finally shut, sleep did not come, only more thoughts about his newly beloved Rei. His mind was tearing itself into pieces trying to figure out how he could fix this problem, the rift that had formed between the two in the past week that had passed since they had traveled to NERV to regain the power of the city. At the brink of sleep is when he felt it, the apartment shook slight, reverberating back and forth like a cell phone on vibrate. Just another one of Tokyo-3's explosions, the ones that had plagued the city and the two teens for quite some time, lack of daily human routine caused some of the regular systems to malfunction and in the more extreme cases, explode. Throwing his fists down at his lost chance to finally get some rest, Shinji tried to remember exactly what had happened.

Rei had not spoken the next morning after the NERV trip. Shinji didn't happen to notice this because he was entirely too involved with his one man conversation, telling Rei how great she was for fixing their power problems and thanking her for lighting up the park even though he knew she didn't particularly care for. He continued his own perpetual conversation without any input from Rei, bragging how he spent all night figuring out the laptop they had brought back. Rei had told Shinji to grab it right when they left, if they ever needed power in a certain district, the wireless ability of the small silver laptop could instantly bring said section to life. Shinji had took it out on the deck with him and tried playing with it, and though it was definitely no EVA, by the end of the night he was able to flip lights throughout any part of the city, on or off and was thoroughly enjoying creating his own light show.

Rei on the other side of the conversation didn't even look at Shinji, she just quietly finished her meal and in mid-conversation she left and entered her room. Perplexed by this Shinji followed her and was about to enter when his fear of all things female took over and caused him to mind his own business. That night at dinner, (Rei had skipped lunch) Shinji once again tried to pull a conversation out of his hat, but after a few minutes of forced conversation, he gave up and let her be in peace. And that's how it went, the entire apartment, even, it seemed, the entire world had gone quiet since Rei had stopped talking, and Shinji spent all his time trying to figure out what he had done wrong, because naturally, in his eyes, it was definitely without a doubt, all his fault.

Rei had actually spoken once in the four days of horrible silence. It had been at the exact moment the painful thought of losing Rei had slipped from Shinji's mind, and he lie on his back in the living room listening to his SDAT, pondering why he still lived in their 3 bedroom, beer soaked apartment, when they could live anywhere, even the huge house that had 46 bedrooms and took up nearly an entire city block in downtown Tokyo-3. The pool by itself was as large as his entire apartment complex, maybe if they moved there Rei would… A shadow cast itself over Shinji's closed eyes, he opened them and looked up, as his eyes adjusted he saw the outline of Rei's face looking down at him, because she was standing right in front of the sun, he could not see her face, just the blues of her hair, and the pasty whites of her skin, and a single long eyelash on each side of her face. Even without her face she was beautiful. Shinji quickly yanked the earplugs out and looked at her.

Without moving, without even seeming to breath, she whispered out,

"What was your mother's middle name?"

"Wha-what?" Shinji asked, surprised at both Rei's lack of knowledge and the question, after two days of silence, this actually almost frightened him.

Rei did not respond, instead she blinked and waited patiently for Shinji to gather himself.

"Uh-um…well…her name…it-it was…Lily."

American? Rei thought, remembering in her studies that it was the name of a flower. Her perplexed look caused Shinji the need to reiterate.

"Well…no-not really. She did not have a middle name, like you and me…but…I once heard father call her Yui Lily Ikari…I think…I think he gave her that nickname when I was young."

Rei nodded, accepting this, and turned to go, when Shinji called out and asked her why she wanted to know.

"Curiosity." Was her answer, and her becomingly cliché act of throwing him an emotionless gaze and walking away. Shinji walked her go, but with a mouth full of cotton could not call after her. He did the only thing he knew how, and putting his headphones back on he cursed himself for his cowardice.

This is what life had become. Walking now, alone, through the grocery store Shinji picked up random items and placed them in his basket, too at war with his mind to really concentrate on what he was purchasing. Ramen, fruit, meat, drinks, cheese, bad eggs, and bad milk, all went the same into the cart that jingled as it shook from its one loose wheel. Shinji had just fallen deeply in love with his blue haired Angel and now what happened. He missed her so, even though she was only in the other room it felt as though she was a million mils away, and Shinji did nothing, but claw at his mind that begged the question: What is wrong with Rei?

YUI

Access Denied.

IKARI

Access Denied.

THIRD IMPACT

Access Denied.

UNIT-01

Access Denied.

Rei took her hand from the keyboard and placed it under her chin, and letting her armrest on Asuka's desk while she stared at the small 12" Apple laptop. It had been 2 days since the incident at NERV, and the file AYA NAMI-05 was tearing her insides apart. She hated that number more than anything, because it meant one thing:

There were more Reis.

Sitting at the Commander's terminal a few days prior, trying to reconfigure the power system, Rei looked lovingly down Shinji who was playing with an empty clip, trying to see how far he could throw it up and still catch it. Seeing this, Rei had an idea, and rewrote the programming so at night not just their apartment would light up, this would please Shinji, and Rei had long since let her emotions dictate on all decisions that involved the young boy. Smiling inwardly she rewrote the program, and after about 15 minutes she glanced down to see a now asleep Shinji laying back on Ibuki's bullet ridden chair, he moved uncomfortable and tried to lie on his side, two bullet head fell from the cushion he sat on and hit the ground like ice falling from a tree, with his headphones on Shinji didn't even notice. Rei did not want to wake him and decided instead to look over her program again once more for errors. Unfortunately, because she was in the Commander's chair, and it was full access, a reminder icon popped up and said:

Check AYAN AMI-05 for biometric stability, overdue by 68 days. Level Approaching Code Red.

Double clicking the program, a box popped up and patiently waited for her to enter a password, neither words nor hints were visible, and the only words that ever appeared were:

Incorrect Password, Access Denied.

Quietly the curiosity of what this program contained ate away at Rei's mind, causing her to enter nearly 30 passwords before giving up and waking Shinji for the long trip home. Shutting herself in her room, this is where Rei has stayed for the past few days. Her mind was a torrent of information, questions, and thoughts. Closing her eyes and lying back on Asuka's bed, she forced every ounce of emotion from her mind, it would be locked away until this decision was solved, she must become her past self to solve this dilemma, because if not, she was still just a clone, and not worthy of Shinji. And Rei just couldn't take that. She was also becoming quite accustomed to being real, and she wasn't going to let the man who stole her freedom for her in the past life take that feeling away from her, even from the grave.

I am no longer myself. Then who am I? Have a just been given pseudo emotions like what the Angel had given me before. No, that is incorrect; the only emotion I received from the Angel was loneliness. What I have now is real, but the Commander had created more of me, more 'husks' that must have escaped Dr. Akagi's plan. I am Rei, but also, Rei-05 is Rei, and I cannot be me without the destruction of me. I must learn more of this Ayanami-05. When I was false, before the coming of Third Impact, I was the third one. Therefore there must also be an Ayanami-04 who is not real. I must destroy them both, or the only emotion they will ever feel is loneliness that is from the echoes of my third self. That is not something I want...No. I do not desire that, her death is simply a necessity.

Rei was herself again, her previous self. Analytical, cold, uncaring to nothing but the task at hand. Sitting up she mapped out in her mind the method of her soon to be mayhem. She would spend all the time it took to unlock the program, find out all there was to know about Ayananmi-05 and the possible Ayanami-04. Then Rei would have to travel to NERV, and destroy her other selves. That would assure that Rei was once again Rei and she could actually be whole again, and be, and deserve Shinji, and embrace her newfound soul.

Sitting down in front of the laptop that she had to seize from Shinji's playful hands the young girl looked around her little Japanese room, the paper walls let in just enough light for her to see the keyboard, Asuka's clothes were long since gone, but with Shinji and her not talking, the room was becoming very reminiscent of her old apartment, her dirty clothes and clean ones were scattered everywhere as were the empty plates of her previous meal. Opening the tiny laptop, she remotely accessed the Commander's desktop, and because this was a secure line, it was just as if she were sitting at his desk with a little lag in response time. Double clicking the reminder once more, the white frosted glass looking box opened, with only a space to type the password in and a glowing silver button to accept. Rei was ready, and began to work.

Three days later, a very tired, and very annoyed Rei laid on her back, glaring at the little ceiling, begging it to tell her the Commander's password. She had put in thousands of passwords, 4,326 passwords to be precise, and all of them had failed. Every ounce of Ikari history she could remember, and everything she knew about all previous projects and NERV in general was entered and each and every time, she had failed. She had even went as far as to force herself to talk to Shinji again, a person which she believed she was inferior to and undeserving to speak with, to ask him what his mother's middle name was, it was a good try, but again, it had failed. She had hurt him when she spoke with him as her analytical self, her cold mechanical demeanor scared the boy, but it was for his own good, Rei could not kiss, touch, or speak with him until she was sure that there were no others like herself, that she was once again Rei, because away from everything else, being Rei Ayanami was all she had.

Believing she was going about this all wrong she thought about the Commander and realized that she was thinking as though he would actually type his emotions out, but the Commander was like what Rei used to be, thusly she simply had to think what she would have used for a password, and continued.

The next day, after another few hundred failed passwords, because she was on a secure line, the computer never locked her out, it simply told her that access was denied and began waiting for her next try, Rei was at her wits end. She fell back, once again onto Asuka's bed, and ignored her rumbling stomach and her eyelids that were like two barbells because of the lack of any sleep whatsoever in the last 4 days. She let her head fall to one side and as her eyes closed she saw, with blurred vision, a thick red book. Stretching slightly, she glanced back at the book, it was a German-Japanese dictionary, when Rei's sleepless brain finally thought about this, she sat straight up, grabbing the book and going back to work.

The dictionary wasn't doing a very good job, the problem with Kaji, Rei thought, is that there were 10 different ways to say everything, and it wasn't until the fifth and final day that she closed in on the password.

Patience.

She entered.

Incorrect password. Access denied.

Another version.

Patience.

Incorrect password. Access denied.

Rei didn't sigh, didn't get frustrated, she simply entered the third and final password.

Patience.

It's third form was accepted, the box disappeared, and at first Rei didn't know what happened, she just looked back to the dictionary and looked for the next word until she heard,

"Welcome Commander, please memorize the following password for your next visit."

HeavenIsEmpty

Windows began opening up at an alarming speed, five video windows, all in real time aligned themselves down the right side of the screen, each with their own heart monitors and readily available statistical application. On the left side audio features popped up, security cams, and password changing programs to every security door from where Rei sat to Central Dogma. Instantaneous phone connections could be established to anywhere in the world, 'hot lines' to all the other NERV factions in Germany, the US, and China, and the Japanese government. This was the Commander's little secret. He could override any system protocol he wished, issue commands to any area in the city, the world, send out EVAs , reprogram them to specific children, even insert the Rei/Kawrou plugs, in all actually, if the Commander would have turned his terminal over to Dr. Akagi, she could have hacked into the MP EVAs. The world was under Gendo Ikari's control, and once again Rei was surprised at the lengths of his reach into the world.

Shinji Ikari was a man without an island. Returning from the grocery store, he put everything away and began to prepare dinner. It was pointless to really put all his culinary skills into his meals because Rei didn't even eat with him anymore. But that did not matter, he was still in love with her, and wanted to impress her in any way he could.

Slinking slowly back into his mind, Shinji began to cook.

There she was.

Rei-04 stared smiling gently up at the camera which was pinpointed at her glass cage. There were two separate glass tubes, just long enough for people trapped inside, but not quite wide enough for them to move around. The false Rei touched the glass slightly, and Rei felt almost as though she had touched her. The true Rei's hand cringed, digging her perfect little fingernails into the desk as she tried to hold back the flow of emotion that was weighing down on her so heavily she could hardly keep her eyes on the screen, it was as though they burned like fire every time the two girls' eyes met.

Seeing herself trapped in the cage Rei felt as though she was going to vomit, this was too much for her to take. She knew fully well that she was one of many, that before Third Impact if this husk died, another would simply take her place, yet she had never actually seen the bodies and truly tried to hide all this information from her mind, keeping the harsh reality in the most unused recesses of her mind. Now though, she could not do this, it was staring right back at her, grinning with a glow of unidentifiable happiness. With nothing but a body, and empty mind, Rei-04 was perpetually happy, curly her lips upright gave her a feeling. Not pleasure, but a numbness, and with the only other feeling being the loneliness that her third self left behind, the husk of a girl chose to dumbly smile at everything she saw.

Rei swallowed hard, it seemed as though her throat had become only a quarter inch thick, and it hurt just to swallow. Her mouth then became dry, and her stomach lurched inside, not understanding, but wanting the get rid of what ever was causing this sickness. Rei swallowed again, this time is was vomit. The glow of the computer screen bounced of the subtle changes in her face and her eyes looked off to the side slightly, she could not bear to look at her false self again. She clicked the mouse to minimize two of the four images that held her previous self, and looked back toward the screen. Even though the picture was gone, she still knew the girl was smiling.

"Misato" Shinji whimpered out as he pulled some milk from the refrigerator, looking sadly at one of the cases of beer. Shinji once again wished he had someone to talk to, anyone…about his feelings for and the current situation with Rei. He wanted someone to talk to, or run away, or leave, or die, or something to get this horrible feeling out of his head! He missed Rei more than anything in his entire life.

The brown haired boy put some carrots on the cutting board and began to slice. He had been trying to create any meal that he thought Rei, being a vegetarian would enjoy, but so far, every attempt at this had failed, she would simply come out at the appropriate time and take her plate without a smile or 'Thank you' and return to her room. Shinji had become actually waiting for this moment every day, looking forward to just a glimpse of his love, it was sad, yes, but so was Shinji.

Looking at the clock on the desktop, Rei was relieved that dinner would be in 15 minutes, she was starving. The thought of seeing Shinji was a plus too, although she knew because of his previous reactions to there being multiple versions of her that she could not talk to him.

Looking around the rest of the secret files that she had complete level 6 access to, Rei's stomach began to calm down slightly. Many of the files where simply statistical values, operation manuals, past reports, and other past projects that did not matter anymore. Rei was actually growing slightly bored when she realized something: The woman in the other tube was alive! She was moving gently because of the bubbles that were released every few moments to keep the liquid from becoming stagnant, and she just blinked. Not smiling, the woman didn't even seem to realize that she was alive. This was understandable, as she was not a Rei and did not have anyone to preprogram her with memories. There was still something strange about this 30-ish year old brown haired woman. It was her mouth, it was very similar. The lips especially reminded her of someone…but whom? Rei subconsciously put her finger over her lip to think, and realized…it was hers! This woman's facial features were almost identical to her own. The lips, face, eyes, minus the color, and jaw were almost duplicate to her own, double clicking the image to bring it full screen she watched the 'dead' nude woman float gently and studied her. There was something written on the bottom of the tube, where the glass met the metal sealant, inscribed in white lettering, but the image was blurry. Rei shank the window and began looking for files entailing any details of this mystery woman. Unfortunately every scrap of information that even was remotely related to the brunette was of no help. About to give up, Rei tried the onboard help system,

"Welcome to the MAGI/NERV assistance manager, how may I help you?"

A female voice asked, the same the had always been the alarm system for NERV and the same that reminded her of the password change. A small clear box opened up for Rei to type in her question, it blurred everything behind it to set itself apart.

Information regarding Rei Ayanami.

A plethora of information appeared in front of her, pictures, audio, video, surveillance reports, Rei's entire lives summed up in one large document, from her first steps to her last sync ratio, everything was there. She read about how Dr. Akagi hacked into the MAGI using her mother's programming skills and destroyed the other husks, fortunately, one more was kept separate in such an occasion in which the others where destroyed, one way or another. That is where Rei-04 came from. She was not special or different, just the next in line. For some reason the real Rei felt better by this information.

Information regarding Aya Nami-05.

AYAN AMI-05 otherwise known as the Ikari-b project.

Almost shaking with fear and anticipation, Rei read on.

Yui Ikari, absorbed into EVA-01 was almost fully cloned. Parts of her DNA surviving from the pieces of clothing left behind gave NERV the ability to fully clone her, unfortunately because of the death of Dr. Akagi (senior) the ability to restore memories and life to the clone was lost. The creature known as AYAN AMI-05 was given this name because memories from the fragment clone Rei Ayanami were given to Ikari-b, thus giving her a suspended life (The ability to breathe, blink, react to sudden movements, etcetera). Although this was a vast accomplishment, the body of Ikari-b, without having more or the original Yui Ikari's DNA, this is as close to human as possible. Ikari-b has been in suspended animation for 15 years and 96 days. Because of age manipulation, she is frozen at the age of 36. She was scheduled for destruction on March 21, 2015. Gendo Ikari moved her to the 'hidden' floor of the NERV center, and all files pertaining Ikari-b were destroyed. To the personnel of NERV, Ikari-b never existed.

Rei finished, visibly shaking, then glancing back at the glass container, she quickly turned to her side, and threw up.

Shinji served the food onto both plates and laid them on the table. Sitting quiet down he soon remembered he'd forgotten the orange juice, something Rei loved, and as he turned around to put it on the table Rei came bursting out of her room. Her eyes were bloodshot red, and her cheeks were pink, tears streaming down her face she threw both of her arms around Shinji and began to sob. Dropping the glass of orange juice that shattered at their feet, soaking into both of their socks Shinji clutched Rei close, noticing the stench of vomit emitting from her mouth, not to mention the speckles of it on her shirt, Shinji didn't even care, and with not really knowing what to do or say as she sobbed, he had not been ready for this.

"Wh…what-what's wr-wrong Rei?" He asked, trying to seem calm, even though her tears were tearing him up inside.

Rei had broken down when she saw the clone of Shinji's mother, she lost all of her senses, and became a complete emotional wreck, and the only thing that came to her mind was Shinji, and how hurt he would be. Not even really feeling as though she was inside of her head, she watched distantly as her emotions forced her way into Shinji's arms, sobbing uncontrollably.

"Y-you…your…your father…" She muttered out between sobs, the analytical Rei hated to see herself like this, she wasn't even making sense, but the emotions overrode any sort of logical speech, and ripped at her insides like knives.

Hearing the word 'father', Shinji's hands both became tight fists. He hated him with all his heart, but the question that begged more than any question before it nagged at him:
What had Gendo Ikari done?