Who is Rei Ayanami?

In the darkness, a pair of red eyes stared lifelessly through the glass.

She floats still, careful not to break concentration. The Commander was watching her. He would never allow any change in routine. She breathed bubbles formed by the orange LCL that surrounded, paying no mind to the void around her.

She can hear them. The giggling. The whispers. Mutterings of jealousy, anger and a hint of bemusement that she was allowed to roam free while they remained behind to be forgotten. To be replaced. She had known she wasn't alone in this dark place, how could she be? The darkness only concealed a truth she already accepted, drilled into her by the Commander. Despair would be the natural reaction at the thought of it, but not her.

Rei Ayanami does not despair. She had a duty.

Commander Gendo Ikari stared impassively at her body, still floating in the tank. He adjusted his glasses carefully.

"The session is over Rei. Your synch test will be in two days."

Rei looked at the Commander, and nodded.

"Yes sir."


Rei walked the street alone.

She knew the path to school, having crossed through it multiple times in months. A turn at the street corner here, go a few blocks there. She would get up early in the morning to get into the train, be arriving shortly. Any danger she would be facing would immediately be intercepted by Section 2 lying in wait.

In truth, Rei did not understand why the Commander ordered her to attend the school. He explained that it was to maintain the pretense of a normal girl, but Rei saw no point to it. She wouldn't receive knowledge textbooks she didn't already know, human contact would be detrimental to his plans, and the teacher was dreadfully boring. The most she did was look out the window to see the grass and trees outside, and even that had limited appeal.

It was an nonexistence she did not care for. Faceless crowds that blended together, the sound of leaves blowing and the wind that felt more real than people.

Nothing in the world would benefit her.

She had the Commander.

Normally nothing was usually what would come up when Rei made this turn. Stop at the lamppost and turn right. No problem. Things should be fine.

A forceful grip on her arm put a stop to that pretense.

"Hey lil lady!" A voice was heard next to her ear. "See, I need some cash right now so if you just cooperate, you get to keep your head okay?"

Rei felt the presence of a knife on her neck. This was a mugging.

It was the first time it had ever happened to Rei, too used to traveling alone. How could this have happened? There was no alteration of pattern.

"Cease your actions." Rei managed out. "There will be consequences for this."

She searched around, but found no Section 2 agents in clear view. Where were they? They should have stopped this mugger before he could even take a step.

"Listen, they're payin' me to do this. Just play along and you can keep your pretty little head on those shoulders 'kay? Put em up!"

THWIP!

The knife on her neck was pulled away. Rei fell to her knees as the criminal had been pulled up by someone. She looked above to see the mugger struggling to get out of the webbing.

"Jumping a teenage girl? So disappointing. Tokyo-3 needs a better class of criminal than that!"

At that, Spider-Man dropped from the lamppost. He dusted off his shirt while Rei looked at him curiously.

"Get me down from here! Fucking bitches!" the mugger yelled from his place.

"Don't mind that fine gentleman, he just needs a bit of a time out." Spider-Man said. He raised a hand towards Rei. "You alright?"

Rei took a hold of his hand and picked herself up. "You're… the Spider-Man…"

"Yup! That's me!" Spider-Man placed a hand to his chest, raising his head up. "I'm your one and only friendly neighborhood Spider-Man, adding a personal touch to your life! Nice to see someone heard of my good name."

"I have… heard of you before." Rei said. "They call you a threat."

"Let's just say my press agent hasn't done a very good job. I fired him." Spider-Man bowed. "Don't worry, I'm not gonna hurt you. "

Before Rei could say anything else, some men in suits pointed guns at the two of them.

"Freeze Spider-Man! You're under arrest!"

"Sheesh, even here I can't ever catch a break." Spider-Man muttered in a frustrated tone. "I'd love to stay and chat but I got an appointment with my neurologist that I can't be late for! Toodles!"

Spider-Man sprang into the air, leaving Rei behind. As several of the agents futilely tried to chase the web slinger, one agent came up to Rei.

"You weren't harmed by that freak were you?" the agent asked.

Rei shook her head in the negative.

"Good. We're gonna keep an eye out for him. Get to school."

The agent ran off to join the others. Rei stared at him as he went, before going back to the direction of her school.

That was the Spider-Man. She had her of him before, mentioned by several of the students and mentioned on the radio as a menace. He was supposed to be a superhero, out of the mangas.

He seemed… familiar, somehow.


Shinji Ikari had joined up with Touji and Kensuke in time for school.

For now, they sat on the tracks. The boys in their class were doing some activities like running and playing basket ball. Slightly uphill, there was a swimming pool where the girls are taking their own courses. There were some boys down hill trying to take a peek, but each and every one were caught and immediately forced to run a hundred laps.

Two days ago, Shinji told a story to his new found friends about a boy who by some stroke of luck or a twist of fate, had been bitten by a spider and received powers and abilities that matched. He told them of how that boy made a mistake that cost the life of his guardian, of how he swore that day he would use his powers for the greater good. He told them about the Spider-Man's encounters with strange and powerful villains, and how each fight made him better and better for oncoming days. He told them of how he survived Kokoro's destruction and received a letter to move here, where the boy would end up becoming the pilot of an Evangelion, the Angel Killing War Machine.

Touji had been impressed with the story, his respect for Shinji being greater than before.

Kensuke, on the other hand, had questions. A lot of them.

"Do you shoot webs from your butt?"

"No."

"Do you eat flies?"

"No."

"Is there a Spider-Woman? If you mated with one do you spit out the eggs before or after she eats you?"

"Kensuke what the hell?! No, no to all of that!"

"Aw man gimme something, you're freakin' Spider-Man!"

"Keep it down!" Shinji placed a hand over his friend's mouth. "Secret identity remember? I really don't wanna deal with the entire school knowing who I am!"

Kensuke removed the hand from his mouth. "Right right but c'mon man there's a whole load of questions one must ask about how a spider-person works! Touji help me out here!"

"He said no, so no." Touji said half heartedly. "Just give it a rest."

"But TOUUJI-!"

Shinji couldn't help but smile. He didn't tell the duo everything, of course. He left out some key parts in his story, such as the girl who's smile he once adored and the conspiracy that caused the second impact and secretly controlled the world. Maybe in time he would tell them, but for now such information would be too overwhelming.

"Dude we're in a once in a lifetime opportunity!" Kensuke almost yelled. "We're friends with a superhero! We could be like his sidekicks or something!"

"Get your head outta the clouds Kensuke, he's got super powers and we don't." Touji shrugged it off. "Besides what can we offer him?"

"Well we could be the guys in the chair!"

Shinji turned his head at that. "Guys in the chair?"

"Yeah!" Kensuke pushed his glassed up. "We hang out at the computers talking to you while you're web swinging! We'd be the Amazing Spider-Man and the Spider-Clan!"

Shinji rolled his eyes. "I'm not gonna put you guys in danger like that! Bad enough the Eva does some damage but-"

"But nothing! You're not getting rid of us that easily!" Kensuke smiled wider. "So can you stick to anything? How much does your spider-sense pick up? Seriously, can webs come out of your butt?"

Shinji was about to say no for the billionth time when he looked up. A familiar pale girl sat next to the fence above the cliff. She seemed to give no thought to her surroundings. She sat by herself, away from the rest of the girls at the pool.

"Oh her." Shinji turned to Touji, who continued. "Rei Ayanami. She's the ice queen of the school. No one knows her, the few that've tried got some harsh rejections. It's like she's some kind of alien."

"Yeah kind of a bitch…" Kensuke chimed in. Then, he got a weird look on his face. "Ah I get it! You're after those boobs!"

Shinji's eyes widened. "What?"

"Oh yeah, that chest-"

Touji came next to Kensuke.

"Ass-"

They both shoved their faces at Shinji's point of view.

"THOSE LEGS!"

"Quiet you two it's not like that!" Shinji nearly yells, just itching to bash their skulls. That it'd be irresponsible for him to do is the one keeping him from doing so. "I'm just… wondering about her…"

"Is she an Eva pilot like you?" Touji said. That would explain a lot, probably saw horrors we've never seen."

"Would explain where the bandages come from too." Kensuke said. He got a little smile. "Do you think we can ask her for nudes-"

With that, Shinji said fuck you to responsibility and punched Kensuke in the face.


"Mmmmm haaaaah! Isn't nice we're all eating together like this?"

Misato drank from her beer can as Ritsuko and Shinji dug into their food. From the taste of it Ritsuko had surmised that Shinji had made them, because the food had such a miraculous taste that made her near cry tears of joy in contrast to the usual absolute disgust and horror she'd feel from what she could only barely bring herself to call Misato's cooking out of generosity.

"I must tell you Misato that the only reason I agreed to this is because Shinji was cooking."

"Yeah yeah, Ritsuko. You got the report about the Angel's core that Shinji cracked?"

Ritsuko pulled out a file from her bag. "Yes. Mother and I passed the data through the MAGI multiple times. Most of the test results came inconclusive but we managed to figure out even though it's made of form of matter different from humans, the actual wave pattern composition of the thing has a 99.89% of resemblance to humans. They're near identical."

"Near identical?" Shinji exclaimed bewilderedly. "No offense but I hardly see any humans that are fifty feet tall and shoot lasers from their eyes. You sure that's what you got?"

"It was, which is the most confounding thing!" Ritsuko grabbed her hair with both hands. "There's so much we don't know about the Angels and we'll never even get a chance to study because they're too busy trying to kill us all! If only there was a way we could save one for study!"

"Pretty sure we'd be stupid if we ever tried to capture one," Misato said. "They're monsters that need to die. That's all I need to know."

Shinji felt something pulling at his pants. He looked down to see Pen Pen, who held out a plate with a pleading look on his face. With a little amused smile, Shinji placed some of the food on Pen Pen's plate, and the little penguin happily hobbled over to a corner to devour that plate in an instant.

"Hey Shinji,"

The boy looked up, to see Ritsuko holding out an ID card.

"I forgot to hand over this card to Rei earlier, do you mind giving it to her tomorrow?" Ritsuko asked. "She's going to need it to get into the base since the old one had expired.."

"Uh, sure." Shinji grabbed the card from her. He stared at the picture in the card, which showed Rei with the same impasse face she had that time they were in the hallway, that time he encountered her as Spider-Man, and even the pool earlier today. He looked at Ritsuko. "Doctor, do you know anything about Ayanami?"

"Oooohhh did my little Shinji get a crush from a picture?" Misato said ever so deviously, delightfully grinning. "Do you need help with a date? I do have plenty of experience ya know!"

"M-Misato!" Shinji blushed. "It's not like that! I was just wondering what happened that she couldn't pilot the Eva the first time I was here?"

"Honestly Misato you can be so immature." Ritsuko rolled her eyes. "As for your question… there was an incident with Unit 00. It went berserk."

"Berserk? What do you mean?"

"For a frightening few minutes," Ritsuko said. "it seemed to have developed a mind of it's own. We lost connection to Ayanami and the Eva started punching at the walls. It nearly smashed us to death with it's hands. Through miraculous circumstance, we managed to eject the entry plug from the Eva, Rei was injured during the ordeal and your father went ballistic."

Ritsuko shrugged her shoulders. "Rei's not exactly normal, Shinji. She's a nice girl, when you get to know her I mean. It's just… she has a bit of trouble with things."

"What kind of things?" Shinji asked raised an eyebrow.

Ritsuko moved her eyes to the side. She seemed to struggle for an answer.

"Living I guess."


Shinji wouldn't understand what she meant until the next day.

The sounds of demolition work permeated throughout the area. The apartment complex had been right next to a construction site, which meant that the area was often busy. It made it a touch harder to land on an area where he could safely change, but Shinji managed that no problem.

No. It was the building itself that gave him pause.

Since he entered, Shinji's spider-sense had been kicking in. The place looked like it had hardly been renovated in years. It was dirty, unsanitary, with a ton of cobwebs hanging around. A single spider descended from a web line, and Shinji could only nod in mutual understanding.

'Where was the room…?" Shinji thought. 'Ah! Here it is.

Room 214.

Shinji gently moved to knock on the door. Seemed like the polite thing to do really.

"Hello? Anyone home?"

As his hand reached the frame, a squeaking noise revealed the door opened by itself.

"What the heck?" He said in a whisper. A panic erupted in him. "AYANAMI!"

Shinji did not question it. He pushed the door open and barged inside.

He was confronted with a spartan lifestyle. The room was bare, without a trace of a personal touch. Not a stack of books, a poster, nor even a TV. Instead, there were the signs of a malnourished being. Trash littered the room, everything was dirty from the ceiling, the tenets of basic hygiene practically ignored.

"Ayanami? Are you in here?" Shinji called out. "The door was open by itself!"

He searched around the place. It didn't seem like it had been ransacked by anyone at least. Was Rei careless? He didn't know. Shinji walked around the room, carefully observing the area. There was strange feeling in his chest. It was… sad?

That seemed appropriate. It was hardly as if he had much himself at Kokoro, but the room was so empty in a way that struck a chord with Shinji. Gendo had never been around for much of life, but he assumed it was because he was uniquely horrible in some way. He didn't think the Commander would put one of the pilots in a dump like this!

From the corner of his eyes Shinji spotted a little case on Ayanami's desk.

'What could that be?'

He reached over and grabbed a hold of the thing. Carefully, the case opened.

Glasses.

'I didn't think Ayanami would need these.' Shinji thought. 'No, I saw her read without any. Wait… are these…'

A flicker of memory.

'My father's glasses. She has them here. But why-?'

"Put that back."

A sharp pang on his chest, Shinji turned around. Ayanami had evidently been in the bathroom the entire time, as she stood over him with only a towel concealing herself.

She stared at him through those passionless red eyes. Shinji realized he was staring, and yelped.

"GAH! Sorry!"

Shinji quickly placed the glasses back on the table, before turning his back away from her. He could hear steps being taken.

"I didn't mean to barge in without permission, but the door was open and… I thought there was a situation."

Ayanami did not respond. He turned his head slightly, seeing the girl clutch the glasses he had been inspecting earlier. She looked at it intensely, inspecting for any flaw.

"They are not broken…" Ayanami said. "Why did you come here?"

Shinji turned back. "Doctor Akagi forgot to give you a new card. I was asked to hand it over to you today."

He took out the card from his pocket and slipped it across the table.

"I see."

That was all she said. Without so much as a whisper, Rei took the card and made some steps backward. Shinji heard the sound of a drawer opening. No doubt she was getting changed.

He raised his eyes upward, towards the ceiling. "Nice place you got here. Personally I like to add a personal touch to my life, but everyone's different I guess."

A brief pause.

"I do not require it."

Shinji crossed his arms. "Maybe. Still, the place is hardly sanitary. Does no one show up to clean the room or something?"

Rei adjusted her shirt. "No one comes here. I was assigned to it by the Commander. I see no reason to doubt his order."

"Fair enough," The boy shrugged. He took a look at the glasses she left on the table. "I didn't know you needed those, Ayanami. I hardly see you use glasses at school."

Rei had finished dressing up. "You may turn around now."

So he did. Rei was in the usual school uniform. She had this… look in her face. Shinji was sure he was being analyzed, but what exactly were her thoughts he could only guess. His spider-sense wasn't alerting him to any danger. He had that at least.

A moment passed, and Rei simply turned to the door.

"There is a synch test at NERV today. We must head there."

Shinji nodded. "Right."


The ride to get there was awkward.

Shinji and Ayanami did not engage in much conversation. Through the subway that took them to NERV all the way to the entrance, the most that would happen was Shinji asking a question and his companion giving short answers that cut the vine of the talk off.

Shinji regarded her. There was something about her that seemed familiar… he couldn't put his finger on it. The first thought was Mayumi Yamagishi, another girl with the most crimson eyes. Considering HERZ's connections to NERV, it would not be impossible for Rei to be another angel hybrid like Mayumi. A clone without a history would be a useful tool for NERV, someone expendable. Replaceable.

Judging by her reaction to the glasses, it seemed Ayanami had a large respect for his father. It seemed he returned it, if she had his glasses kept in her room. While there is reason for his father to cultivate trust on him, that doesn't explain the shoddy room she was left with. Would it not behoove the Commander of a military organization to at least keep an incredibly important target like an Eva pilot in a secure location?!

As Rei swiped the card on the terminal, Shinji decided to give the talk one more go.

"Today's your synch test right? Are you scared in any way?"

Rei placed her hand on the railing, as the escalator descended the two into the depths of the NERV base.

"I am not. The Eva will accept me, and I will pilot it. There is nothing else to it."

"You sure about that?" Shinji asked. "I mean, I heard yours went berserk and nearly punched everyone to death. I wouldn't blame you if you were at least a little concerned."

"It does not matter. The Eva is functioning, and I will pilot it."

"Suit yourself." Shinji shrugged. "Even now those things still creep me out. Makes me wonder the loonies who came up with them."

A brief pause.

"Are you not the Commander's son?"

"That I am."

"Do you not have faith in your own father's work?"

Shinji grimaced. A tight grip on the railing betrayed a maelstrom, but he swallowed a lump that formed on his throat.

"I trust him to do his job. That's all I can say."

Ayanami sharply turned around. For the first time since he's seen her, Shinji saw a gleam in her eyes. Anger.

"You do not respect him."

Well now. He let out a sigh.

"Ayanami, I don't really know my father. I haven't seen him in years, even the few times we met there was hardly a conversation. As far as I know he left me for his job and never attempted to reach out in the years since. Except for one letter. One. What did it say? Come. Not an apology, no explanation, not even a freaking post card. Like I was some kind of gopher at his beck and call. As a Commander, he seems to be do an okay job at not getting us all killed. As a person… what can I say about a person I hardly know? If he wanted trust, he should have said something sooner. If he wanted faith, he should have done something to earn it. Now it's too late. Far too late."

Silence.

The two kept descending down the escalator. They reached the end, landing on the floor where the locker rooms are. They walked down the hall.

Shinji was just surprised he didn't get slapped. She looked ready to knock some sense into him, but she seemed to have relented. Instead, her face was introspective. Ayanami was contemplating something.

"Your father saved my life." She spoke at last.

Shinji blinked. "He did? When?"

"At the time of the previous synch test, after Unit 00 went berserk, I was injured in the entry plug. My wounds left me unable to get up, but the Commander had broken away the plug's entrance and saved me. His hands were burned in the struggle, which is why he wears the gloves he wears now. I have faith in him, Ikari. He will not fail."

The two stopped. The boy's locker room meant that Shinji had to get in as Ayanami separated. He turned his head.

"If you say so… good luck."

He shut the door behind him.


Shinji sat in the entry plug.

The synch test had gone under way. Unit 01 no longer made him feel an unhappy presence at the back of his mind, even as he recoiled from the taste of blood. His spider-sense had dulled, leaving only the faintest buzzing in his ears. The entry plug felt… warm this time. Shinji told himself not to get too used to it. The Evangelion is a beast, the product of men's hubris. He had to tread carefully, or risk disaster. Unit 00 had been proof of that.

Unit 00 was in mint condition all things considered. It's orange hue is not as gaudy in appearance as Unit 01 was, it's armored head resembling a cyclops with it's one eye. If Unit 01 resembled a demon, Unit 00 looked more like a machine. It was less human, but somehow it made it less off putting than Unit 01. The Uncanny Valley effect it seemed.

Through Unit 01's eyes, Shinji could spot Ayanami coming out of her entry plug, being greeted by his father.

The two of them were having a conversation. Gendo was smiling as he talked. Ayanami… she was smiling too. She lit up with a faint blush.

Shinji frowned at the sight.

'He's smiling at her… she's so relaxed around him.' Shinji thought. 'I've been selected to be a pilot a long while, but he left me and raised her.'

He knew it as irrational. Shinji accepted long ago that his father would never care about him, and given the shady dealings NERV have under the table he wasn't sure if it would have been a good thing if he had stayed. Even so, that his father showed more affection to a stranger, some girl he never knew, over him…

The blaring red alert signals shook him from his thought.

"ANGEL INCOMING. SECTOR 37!"

"Shinji we're sending you out!" Misato's voice came from the comm link.

The boy nodded. "Right!"

With that, the Eva launched. As he felt the turbulence, Shinji felt a nasty set of headaches with a buzzing ringing in his ears.

'Something's wrong!' Shinji thought. 'Spider-Sense was never this intense during launch. What's going up there-'

A searing pain welcomed him to darkness.


"Shinji… SHINJI!"

The boy opened his eyes. Shinji clutched his forehead as he felt a set of arms surround him.

"Oh thank God you're okay!" Misato cried out. She put a hand over his forehead to make sure he was safe. "Still warm but you're alive!"

"Ugh, what happened…?" Shinji's eyes widened. "The Angel!"

"It is currently immobile as we speak."

Doctor Naoko Akagi strode her way into the room, her four mechanical arms slithering in synch with every step. Misato and Shinji glared at her, to which Naoko could only scoff. He let go of the bag she was holding next to the two.

"The Angel released a drill burrowing it's way into the GeoFront." Naoko continued. "The MAGI have calculated that it would accomplish it's task by nightfall. I have you have a plan of Action, Captain, or else we'll be facing a problem bigger that one fallen pilot."

Misato got up from the chair. "I'm working on it, doctor. Shouldn't you be working at the controls?"

"Ritsuko's already handling it." Naoko said. "I came here to check up on Pilot Ikari to make sure he didn't suffer any more side effects. Shouldn't you be at tactical where everyone else is?"

"I needed to see Shinji." Misato said. "A pilot down could mean the end of the world. I'm sure you know that."

"Oh yes…" Naoko sneered. "Well now I need him alone for signs of contamination. Is that clear Captain?"

A silent conflict. Misato stared down the doctor, not wanting to leave as Naoko held a grin that even a snake would be abhorrent.

"Fine." Misato turned to her ward. "Shinji I'll be back later for the operation. Make sure to rest okay?"

Shinji waved Misato off. "Bye Misato, I will!"

Misato smiled at him. She walked outside of the room, leaving Naoko and Shinji alone.

"A little bird told me you were speaking with Rei earlier." Naoko said.

Shinji narrowed his eyes. "What's your game Akagi?"

"Nothing. Nothing at all." Naoko grinned. "I hardly suggest you do that, but your misguided sentimentality will probably cloud your judgement anyway."

"I don't know what you're talking about." Shinji asked.

"Red eyes, a cruel father. Please," Naoko said, "I know exactly what you're thinking and Rei is nothing like that. She is thoroughly in your father's hands. The minute you even try she'll only end up hurting you."

"Shut up." Shinji said. He moved slightly making part of the bed sheet fall to his waist. "You don't know anything."

"I'm not sure you understand." Naoko raised a finger to her chin, scratching it. Her hand closed into a fist and placed her chin on it. "She's nothing like her."

In an instant, one of her mechanical arms caught a punch in midair.

"I mean what I said." Naoko barely even reacted. "If you want proof, head down to Terminal Dogma. You'll see who she really is."

A pause.

Shinji lowered his arm. "Where is it?"

"Excellent." Naoko grinned. A mechanical arm carried the bag she came with. "You'll need this."


The air vents were tight.

Was it insulting he was easily goaded into it by the doctor? Yes. Was he a gullible moron for believing her? Probably. Was this in any way a good idea? No.

Shinji was dressed in skin tight long sleeved clothes, with a mask that had two eye holes. Using his Spider-Man costume would get him in trouble… well, more trouble than he already is if the Section 2 ambush was any indication. A black suit could lend him some plausible deniability. Last thing he needed was to get shot again. Hopefully he wouldn't have to use a black suit much, it's not suited for him.

He silently praised the ventilation system for being wide enough to fit him. Shinji remembered the directions Akagi provided him. If it was right, it would take him to Terminal Dogma, located deep underneath the Geo Front. It was a classified location most NERV personnel, not even Misato, had access to.

At this point, Shinji's curiosity had been peaked. What was down there? What secrets had the Commander locked away from prying eyes?

Only one way to find out it seemed.

'There!'

Shinji noticed a light coming from the right. He crawled through it, to find a grate blocking his path.

SLAM!

A simple punch broke through it with ease. Shinji nonchalantly got out from the vent. He inspected the area.

The darkness of the area gave him flashbacks to the first time he had first witnessed the Eva. A sneaking suspicion that gave way to horror. Shinji tip toed across the hallway, careful not to make too much noise.

His body shivered before his brain could process it. There was a presence in the oom. Someone, or something was watching him. His spider-sense did not buzz in his ears, and yet he felt afraid. He raised his steps ever so slightly, his fear overwhelming. Whatever was here was vast and unknowable, a sun compared to his insect. Being near he, she, it, made him afraid.

GET AWAY FROM ME

-an ocean of red-

HOW PATHETIC

-strangling-

I HATE YOU

-you're disgusting-

'Please don't find me,' Shinji thought, 'Please don't see me. Don't see me…'

His hand found a doorknob. He shook it sharply, opening and pushing himself beyond the door.

Shinji let out a sigh of relief. He turned around-

and found an exact replica of Ayanami's room.

"What?" Shinji blurted out in confusion.

He inspected the room. Every detail was exactly the same as the original, down to the horrid living conditions.

"Stranger and stranger… But I'm still no closer to finding the truth!"

Shinji noticed a door to the left. Carefully, he walked over to the door and opened it. The room was also dark.

"Son of a- is Dad so cheap he can't afford the electric bill!?" Shinji said. "Where's the light switch in this place? I feel something right over… here!"

CLICK

"AAAAAAAAAAAHHHHHHHHHH!"

In the orange glow of the room, there was Rei.

and Rei.

and only Rei.

Only glass separated Shinji from a multitude of bodies with the name and face of one Rei Ayanami, all staring at him from the tank, which was filled with LCL. The blank stares of the Rei he knew felt positive compared to the giggling, goofy smiles on the myriad Ayanamis. They did not speak, only whisper vague incomprehensible mutterings, signifying nothing. They were soulless husks that made even a corpse seem alive.

Shinji could only gaze in astonishment over the horror he sees. He had his suspicions about Rei before, but…

"This can't be real… what… what is this?" Shinji muttered out. "What is this?"

They were laughing. Laughing at him, for daring to appear in their domain.

As crazy as the sight was, Shinji had enough sense to feel the spider-sense. He jumps into the ceiling.

"Doctor Akagi is helping her mother with some data test. We will begin the test early, Rei." Gendo said as he walked inside with a naked Rei. "Step inside."

Shinji could only stare as Rei went inside of the capsule in the center of the room. Gendo pressed buttons into a console and the capsule started filling up with LCL. The myriad Reis continued their little heartless giggles.

"Captain Katsuragi's plan has a low percentage range of success, Rei." Gendo said. "The Third Child will doubt his role. You will need to be ready for the mission."

"Yes sir." Rei said from the tube.

Shinji found himself in a crap situation. If he was in trouble before, then his father would surely kill him now. So Shinji waited.

With the capsule full, Rei floated in the LCL. Vital signs and DNA signatures were monied carefully on the computer screens. Gendo kept his eyes on Rei, as if expecting any moment she could disappear if he glanced away even for a second. A tension was brewing.

"Commander," Rei spoke. "May I ask a question?"

"Hm? Of course Rei."

"Yesterday I had been attacked by a mugger. Section 2 did not come to save me that time. When Spider-Man interfered, they came immediately."

"Ah yes. I staged it." Gendo said.

Red eyes blinked through the glass.

"Why?" She let out hesitantly.

"You have to understand," Gendo pushed his glassed up. "This so called Spider-Man is a nuisance. He has abilities that could interfere with NERV's mission to fight the Angels, Rei. He could very well be able to infiltrate NERV and we wouldn't notice."

'Well he wasn't wrong there,' Shinji thought, watching this unfold.

"I… I see…" Rei said. She closed her eyes.

"Very good Rei. I will place you under for the time being. Doctor Akagi will be with you shortly."

Gendo pressed a button. Rei's body started relaxing in the LCL, as Gendo turned around and left the room.

Her vision dimmed just as she saw a figure dropping from the ceiling.


"You saw it didn't you?"

Shinji could practically feel Akagi's grin even as her back stayed turned to him.

"The tank terrified me too" She said. "So much made sense afterward, but back then? I was shocked at the extent Gendo was willing to go."

Shinji narrowed his eyes. "What the fuck was that and how was Father able to get away with any of it?!"

Naoko's mechanical claws open and closed. She turned around, for once looking haggard, as if she was weary and tired of life.

"Rei Ayanami is an artificial being, the first attempt at mixing human and Angel DNA. The breakthrough with her led to SEELE pooling resources and forming HERZ to pursue further applications for genetic experiments. Some of them were to be used for the Evas, but were also tested for possible military applications in the West."

She breathed in and out.

"The Angel DNA came from Lilith, the Second Angel. You might have seen her downstairs, or felt her."

Shinji remembered the presence that sent him into a panic attack. The thought he was so close to an Angel…

"What about the human DNA?"

Naoko smiled. It was a rueful smile. "The human in the equation was Yui Ikari."

The boy fell to his knees. His eyes were close to watering.

"M-mother?" Shinji wobbled out. "No… no…!"

"Rei was a child when I met her." Naoko let out a dark chuckle. "The moment I laid eyes on her I thought I had seen a ghost. She looked so much like Yui, and Gendo so proud of her, that I had to find out the truth. I never did at the time, my affair been exposed and I was trying to save some trace of dignity. SEELE let me go and placed me back head scientist, he took me down there…"

One mechanical arm punched a wall, leaving a dent.

"I should have known Gendo would never have a place in my heart for me… all he care about is Yui. He'll hurt anyone and do anything to get his wife back, no matter the cost. Rei just another tool in his quest to do that, nothing more."

Shinji didn't say a word. The revelations are still sinking into his mind, paralyzing him.

"Katsuragi came here earlier." Naoko said. She tossed Shinji the plugsuit. "She has the plan ready so I cleared you for piloting."

She opened the door and left, leaving Shinji with his thoughts.


Shinji adjusted his plugsuit.

Misato had detailed Operation Yashima. The Fifth Angel, Ramiel, remained in the same orbit drilling into the Geo Front. Anything that got too close would be immediately wiped out by one of Ramiel's lasers. With permission from the Government, NERV managed to put together a Positronic Rifle that drew power from all over Japan and fire a shot at the Angel's core and obliterate the creature. Shinji had been chosen for the mission due to experience and the damage to Unit 01 preventing it from doing too much other than point and shoot. Rei will be backing him up with a shield in case Ramiel fired.

He stared at Rei, who sat next to her Eva. The operation won't start for another hour or two.

She was a clone of his mother… the sheer lunacy of it was hard to comprehend, He couldn't picture what his mother looked like, or how she was. The most he could remember was a gentle feeling born from a distant memory, and the trauma of it having been taken away.

It was bad enough when he knew Gendo was working for a conspiracy bent on assimilating the world. That he created life from metaphorical clay and make… her… that troubled him more than ever. Shinji didn't know how to feel about Rei. He'd be lying to himself if he didn't feel Mayumi in Rei. He wonders if it was a good idea to befriend her. Is he using Rei as a proxy for Mayumi? Was Naoko right all along?

Was she just some…?

"You won't die."

Shinji raised his eyebrows at that. "Hm?"

"You had a worried look on your face." Rei said. "You wont die."

"Oh… well thanks Ayanami." Shinji responded. He took a glance at the side. "Can I ask you something?"

"Hmhm."

"Why do you pilot the Eva?"

Rei thought abut it.

"I am bonded to it."

"Bonded?"

"Yes. My bond to people."

Rei turned to Shinji.

"Why do you fight Ikari?"

Shinji blinked. He didn't expect the question. A little sigh blew from is lips.

"My teacher, Yamashiro… he wrote something once and I stuck to it ever since. With great power there must come great responsibility. I don't want to be a pilot, not really. It's scary to be out here fighting giant monsters that tower over me and can ruin my face. But if I just stand there while an Angel is attacking? If I was the only one in the room who can fight them off? I'd feel horrible if I caused friends like Touji, Kensuke or even Misato to get hurt, much less cause the end of the human race."

"You have people you fight for." Rei said. "I have nothing."

She got up from the platform.

"I will protect you. Good bye."


Shinji regretted everything.

He had missed the first shot, causing Ramiel to start blasting him but Unit 00 had blocked it with it's shield. With the second shot obliterating the blue cube Angel's core, Shinji got out of the Eva as fast as possible and raced to Ayanami's plug.

He had no time to be careful. He grabbed the opening and ignored the pain from the heat. He can take it. He smashed the thing open and found Ayanami resting in the plug.

'Ayanami is not a clone,' He thought. 'She's not Mayumi or my mother or a tool. She's a girl who needs help, as much a victim of Father as I was.'

"Ayanami! AYANAMI!" Shinji yelled. "Are you alright?!"

"Ikari…" Rei let out, barely breathing.

She raised herself upwards, staring at him. Tears were welling up in his eyes.

"Rei…" Shinji said. "What you said up there wasn't true. You have me, your fellow pilot! We'll protect each other from now on, okay?"

Rei stared at him, almost confusedly. She had never seen someone cry before… not for her sake. The moment was almost exactly like when the Commander saved her life before. It made her happy then that he would go out of her way to save her. The memory now seemed false, as the Commander was willing to let her die for his own plans. She felt more at ease with Pilot Ikari's own rescue. It was familiar…

"I am… sorry." She said. "I don't know what to do in this situation"

Shinji smiled at her. "Times like these, I smile because I'm glad to be alive. Why don't you give that a try?"

When she did, it felt like the most natural thing in the world.

She had Shinji.

Author's Notes:

I hope everyone's safe from the coronavirus. Quarantine can drive people nuts, so have this chapter now!

I had to think about the way I should approach this chapter, since the events from canon were hard to find plausible deviations for. Then I figured it out: do it like a mystery! We the readers already know that Rei is a clone of Yui but Shinji doesn't! With that in mind it made sense to structure the chapter into a puzzle for him to solve.

I think my favorite moment to write was Naoko and Shinji's last talk about Rei. To Naoko, she is just another tool of Gendo but Shinji is able to see her as a person and someone to help, love that sort of contrast between hero and villain.

You might have noticed I just skipped the Ramiel fight. Unlike Sachiel which demonstrated how becoming Spider-Man made SHinji better at combat, or Shamshel which needed to show events like Shinji's anger attack and Touji and Kensuke in the plug I couldn't find a way to make the Ramiel fight interesting or different. Besides, the story this time wasn't really about an Angel battle.

Spider-Man Life Story is super dope guys! One of the best I've read about him, especially the ending.

Anyway time for answering some reviews:

Plmnko: I'll be honest, I'm not sure. I have up to the Zeuriel/Unit 01 absorption planned out and ready, which is up to Chapter 31. A rough estimation would be around 50. Probably less. I hope this helped!

Pokkon: I mean Naoko murdered people lmao Ritsuko's got a right to be upset.

BlakLing: He will not.

Rigby from the Park: Shinji will update his costume accordingly. He technically fought a non-spidey villain before with Yashida, but I plan on keeping it centered around Spider-Man villains. It's his story after all.

Derrick Brooks: Yeah Shinji saved lives but he did so in a way that, if he wasn't lucky, could have ended in disaster. In both canon and this fic Shinji wasn't acting right, and in here he accepted what Misato said because after thinking it over and almost losing Touji and Kensuke again he decided she was right and apologized.

IceyStream: Now you have it!

RealRemainder: Well I hope this chapter didn't disappoint in the deviations department.

Huagh: You'll get to see Touji and Kensuke helping Shinji out next chapter!

Holy Goblin: pfffffft BAD Gobby! No resurrections for you!

See you next time for next chapter: The Menace of MYSTERIO!

Omake by Johnny Freeman:

Shinji and Rei stood still as the elevator took them up to the platform. He's been feeling uneasy with the host of revelations regarding Ayanami, but these thoughts clashed under the severity of the battle ahead. He had a lot of questions but maybe not enough time for all the answers, so he had to decide right now.

"Ayanami?" he asks.

She glanced it him. There was no change in her expression.

"If we don't make it, I have to ask a question..."

Still silent.

"Ayanami... Why do you live in a crack den?"

Rei blinked.

"Excuse me?"

"Well..." Shinji scratched the back of his head. "The place you're living in, it doesn't look very good. I mean, you work with NERV too! I can't imagine why they put you there when you could be living somewhere nicer."

Rei thought about it. "I had no other alternative. All other living spaces were sold."

"Oh," he exclaimed "I see!"

There was that brief exchange of silence between them. This elevator ride felt stretched out, making either of them wonder whether it was intentional or maybe NERV's funding couldn't cover all of the facility. It was probably the latter, given the cheap lighting in Terminal Dogma. In the meantime, Shinji had one more question to ask.

"No offense, Rei but... Do you sell drugs?"

Rei's gaze returned to him. The expression changed from a blank stare to an intense glare. If he didn't any better, Shinji would have thought he stabbed her puppy or something.

"Who told you about that, Pilot Ikari?" she asks, the monotone sounded just a bit offended.

"No, It's not- I mean, some of the guys in the school think that- I mean, well you see-"

He could see the subtle fury in her eyes as she was stared him down. If looks could kill, Shinji would've been reduced to ashes before the elevator reached the top. He expected her to uncharacteristically yell at him for believing the lies made up about her and started beating him to death with a pogo stick.

Instead, she just turned away and remained silent looking at the elevator doors.

DING!

"No." she replied, before walking off to the locker rooms. "I will see you soon."

Shinji felt... Unnerved by the experience. He tried to shake it off as best he could as he went ahead to his locker room.

Meanwhile, Ayanami evades Ikari long enough to pull out her phone and dial a number. After a few rings, she spoke.

"Joji, It's Ayanami. We might be compromised."