He felt her. He didn't know how or when, but he did.

Not long into the battle with the Angel, Shinji had been grabbed by its hand and stabbed repeatedly through his eye. He was then blasted back into a building and his eye bled without actually bleeding. He felt agony from it. Phantom pains where none existed. Wounded.

Even with Misato's guidance, the Angel was too strong for him. Shinji knew for a fact that he would die here, as his father had planned.

'Is this what you wanted, Father?' He thought with bitterness. 'You tricked me into coming here, and now you get to see me die.'

The Angel went to approach him again and-

And-

It was then when the Entry Plug was surrounded in a swirl of rainbow colors, not unlike when he first came in. Red, green, blue, purple, yellow, Shinji's eyes tried to catch all the colors but to no avail. He just tired himself faster for doing so. As he shut his eyes, he felt arms surround his body from behind.

"But… what is this?"

It was a warmth he remembered, a distant memory. But it was impossible. She shouldn't exist in this time and place. Not in the machine.

He opened his eyes and turned.

A translucent shape, strange and familiar, laughed at his dumbfounded look. She- Shinji didn't know how, but he knew she was a woman- she was a specter, unable to do anything more than watch and feel. Anything more would be too much effort, and create problems down the road.

Even so, Shinji couldn't help but welcome its presence. She was safe.

"Are you…?"

A pale finger shushed his lips. The ghost smiled at him.

"Hahahahaha… finally… you're here…"

Suddenly, a memory flashed in Shinji's mind. He was looking up at a bright light, with two large shadows gazing down on him. They were both warm, even if Shinji couldn't see who they were.

"What do you think we should name him?"

Shinji blinked. Mother…?

"If it's a girl, we'll name him Shinji. If it's a girl, we'll name the baby… Rei."

Father? This was from when he was born? But how was this possible? Where did that come from? Why did he remember it now?

Shinji didn't know. As the woman embraced him, he closed his eyes again to try to forget what happened…

Before he woke up.

The first thing Shinji saw pitch white. The light blinded him for a full minute before his eyes properly adjusted to the sight. He didn't remember anything after that moment in the plug. Did they win? Did he lose? Where was Misato? Where was he…?

He wasn't wearing his uniform, Shinji realized. He felt the material on his body, finding he was in a hospital gown. He must have been knocked unconscious at some point before being taken to this room. If he was in the hospital, that meant humanity was still alive.

Shinji leaned his head back to the pillow, with only one thought vocalized in the empty room.

"An unfamiliar ceiling."

They won, but Misato didn't feel happy.

Shinji hadn't done well in his first sortie. How could he, when he only learned about his job for the first time the other night? He was throughly thrashed by the Angel, to the point Misato was sure he would have died- along with the rest of humanity she realized- until the Eva suddenly went berserk and turned the tide of battle. It was a miracle he survived, let alone defeated the Angel.

None of it was thanks to her. Misato promised she would guide him in the fight, but couldn't do anything but watch the one-sided slaughter. It was all she could do from breaking down over sending the boy to his death, especially when she was the one that convinced him to do it. She was more than relieved to find out Shinji had been okay and with no signs of mind contamination. He would be checking out of the hospital in a couple of hours.

After spending the day overseeing clean up, listening to the news cover ups and Ritsuko's data analysis, she figured she could get a minor victory by requesting Shinji be taken out of the piloting roster. It was her other promise to him, one she hoped she could keep to compensate for what he went through.

Unbelievably, the boy's father dashed her hopes right out the window.

"Captain, we cannot allow the Third Child leave the city. He is too valuable an asset now."

Misato frowned at the Commander's uninterested dismissal. He said it so plainly, without a drop of concern. Something lit in her.

"Sir, he's not fit for combat. You saw what the Angel did to him out there. We have other pilots. In fact, we should be getting Asuka over here asap. There is no-"

"Request denied." Gendo stated. "With the First Child still in recovery, we will need all available pilots on hand to defeat the Angels. The Third Child has been found, so you will oversee his training. That is all."

"But sir-" She tried again. "He barely managed to get the Eva moving. What if an Angel attacks tomorrow? We don't have anyone on hand!" A thought came to her. "Can't we get one of the pilots from the other branches then? Someone like Vincennes would probably sync with Unit 01 better than Shinji."

The other person in the room shook her head. "I'm afraid to tell you this, Captain, but he's the only one who can pilot that Eva."

Misato finally looked at the Sub-Commander. Mary Iscariot brushed off the hair from her glasses, giving Misato a sad smile.

"What do you mean by that, Sub-Commander?"

"It's as I said." Mary Iscariot responded. "We tried to sync Rei with Unit 01 not too long ago. It wouldn't accept her. Same goes for other candidates we pulled from the Marduk Institute. So far, Shinji is the only one with a sync ratio high enough to meet Unit 01's standards. We can't let him leave even if we wanted to."

"… you're serious?" Misato kept her voice leveled. "Why wasn't I told this?"

"Need to know basis." Iscariot said. "Take it up with the Committee if you'd like. This is just how it is, Captain. If we could let him go, we would. Like the Commander would say, we have no need for useless pilots."

Gendo gave Iscariot a look. She returned it with a smirk.

"Your words, not mine."

"…"

Misato elected to ignore them. She placed a pair of papers on the desk.

"Fine then. I hope you're willing to help me on this then. Ritsuko- I mean, Dr. Akagi informed me Shinji will be living alone on the base. You won't be taking him in?"

Commander Ikari sighed.

"You saw how he was. He wants nothing to do with me. I, for my part, want nothing to do with him. It'll only be an inconvenience to us both."

"… so that's how it is…" Misato breathed in. "You won't mind if I take him into my custody, then."

Gendo's eyes widened slightly, not expecting such a thing from his subordinate. After a moment, he pulled out a pen.

"If that is your wish. Request approved."

He signed them with no fanfare. Misato gave him a nod, before turning around to get the paperwork approved through the appropriate channels. As she left the room, Sub-Commander Iscariot looked at her superior.

"You knew she was only ever going to accept Shinji. Why didn't you bring him in sooner?"

"I didn't want him involved." Gendo turned his head toward her. "Tell me, Miss Iscariot. Why didn't you take Shinji in yourself?"

Mary gave him a rueful smile.

"He had enough of Yui to make me sad… and enough of you for me to resent him."

Gendo nodded.

"There is your answer. There is nothing more to be said. Captain Katsuragi will no doubt do a better job with him than I ever could."

It didn't take long for Misato to find Shinji.

He wasn't in his room, but in the hospital lobby. Misato took a moment to observe Shinji, now that he was alone. He had an SDAT player on his lap, earphones plugged into it. He had a serene, yet sad expression on his face, as if this were the only way he found comfort. In a moment, Misato watched him clench his hand and opening it as if he were trying to feel something. She wondered if he felt anything from the fight the other day, or if this was in response to something else. He wiped something from his eyes.

She sat in the bed quietly, unable to speak. Her couldn't tell the doctors about her Father, what he did with her or the giant made of light that killed him. No one to save her from the deafening silence of the room. No matter how much they wanted to help her, she couldn't let them in.

It had to be something wrong with her. She was a dirty child. A bad child.

Why else would she suffer like this?

Misato frowned at the miserable boy in front of her. He wasn't going to find relief any time soon, so she had to be the one to make him feel better. She approached him with purpose.

"Heya Shinji~"

Startled at the new arrival, Shinji panicked before realizing it was her. He took out the earphones to really look at her.

"Oh, hi Miss Katsuragi."

He tried to smile, but it came off as an empty gesture. He wasn't used to dealing with people, Misato surmised. Not too surprising given his situation. Still, he didn't shrink at her presence. Clearly she was doing something right.

"Nice to see you're up and about so soon. I told you call me Misato."

"I will, I guess…" He looked down at the ground. "They gave me the all clear… I didn't want to stay in the room. I don't like hospitals."

"No one does."

Misato bit her lip. How was she going to explain it to him…?

"I tried talking to the Commander about removing your pilot status."

Shinji became sullen at her tone. "You're not going to let me go."

"Unfortunately, you're the only one who can pilot that Eva." Misato said. "We're going to get reinforcements soon, but the Commander made it clear to me you won't be able to leave the city until the Angels are gone. I'm sorry."

Shinji clutched his head. Of course. To his Father, he was just a tool and nothing more. There was never going to be a choice for him.

"On the plus side, though! They were going to leave you alone but… I actually asked them if you could move in with me. They said yes!"

He looked at her with surprise- in a manner similar to the Commander earlier, Misato noted. He blushed and looked away.

"R-really? I mean, you don't have to do anything like that. I'm used to living on my own…"

It broke Misato's heart to hear that.

"You shouldn't have to live alone, Shinji. Really, it's no big deal. I like you lots already."

Shinji smiled, a more genuine one. "You do?"

"Yeah! Trust me, you're gonna love being roomies with me." Misato laughed. "Oh, and don't worry. I'm not gonna make any passes at you or anything like that. Ritsuko'll kill me if I did."

He wisely kept his mouth shut about the picture.

"Why don't I show you around? You're going to be living in the city, might as well get used to the terrain."

Not long after, she took him to her Renault- her poor, broken, Renault that she only got two weeks before and was now in desperate need of repairs thanks to those godforsaken Angels, she hated them so fucking much- and drove him to the supermarket to get groceries.

Shinji didn't say much of anything throughout the ride and the shopping, which was fine by Misato. She wasn't sure what else she could say. He clearly wanted some time to think for himself, and she let him. While they were waiting in line to buy food, some of the customers began to whisper behind them.

"My family and I are moving out of the city. We almost died back there, the Eva was no help!"

"No kidding. I need to know we won't get killed with those monsters out there."

"Yeah, what were they thinking with that?! Utterly stupid. The pilot must be a reckless moron if he was joyriding like that…"

"Absolutely. Tokyo-3 is a horrible place to raise a child."

Misato heard them, and saw the way Shinji frowned. She knew she couldn't let them be the final word of the day.

Without a second thought, Misato took Shinji up one of the highest peaks of the city. A road off the side of a mountain, the edge of a cliff which gave them a clear view of Tokyo-3.

"Why are we here, Miss Misato?"

"Just hold on a sec. Something cool is going to happen."

Shinji didn't know what she meant by that. Then, he saw it.

Buildings he passed by earlier began to lower into the ground. Taking their place were taller, more advanced skyscrapers that reached higher into the sky. The skyline became livelier, with bright lights and people thriving in their new environment.

Thinking Shinji would still be staring at the city, Misato said-

"Look at this, Shinji. This is the city you protected."

However, she turned her head to find him looking up at her in awe and amazement. She couldn't help but beam with pride.

"We'll all be counting on you."

Eventually, they finished their tour of the city just as night descended upon them. They arrived at an apartment complex within the neighborhood.

Shinji elected to hold the groceries and let Misato lead the way. She knew her way around here, unlike him, and he already felt useful helping her carry the bags. Misato whistled at the door.

"Oh good, It looks like they delivered your stuff already! I just moved in here the other day myself so I still have some unpacking to do myself."

The door slid open as soon as they approached. Misato entered the apartment first.

"Welp, come on in! This is your new home now."

Shinji looked down at the floor, then back at Misato. Home… He lived in a house for years, but he hadn't known a home for years. Can he trust this? Will it be ruined? He didn't know. Reluctantly, he stepped inside.

"I'm… home."

Misato couldn't keep the smile off her face even if she tried.

"Welcome home."

Misato had to admit, it felt nice to have someone to talk to at home.

Sure, she could feel the subtle judgement Shinji gave her once he saw the chaotic mess around the apartment, magazines, trash and beer cans on the floor without care. She couldn't say she enjoyed him looking at her like a lazy slob, but she supposed she had it coming for agreeing to take him in without preparing the apartment first.

She also knew that the yellow tank top and denim shorts were a bit tight around her body, so the teenage boy in Shinji was bound to give her some glances. She caught him once or twice just now while eating. Not that she minded, of course. Boys like him could use service every now and then.

Misato did mind the way he slowly picked at the food in front of him. The ramen wasn't even her cooking this time, it was microwaved left-overs! Was he seriously that picky with his meals? Or was it that they came from her? She just wanted to do some nice things for him, why did he have to be so mean to his new guardian on the first day?

At least she got a tiny bit of revenge on him. Not only did she force him to eat her food, but she also tricked him into playing rock paper scissors fight over the chores. She won most of the matches, which meant the cleaning, cooking and laundry now went to him. Serves him right, let's see if he can do better than her in that regard!

The last time she had this sort of company was with Asuka, but that was a long time ago… Would she even want to see her right now?

'I hate you, hate you, hate you, HATE YOU!'

Downing a can of beer before swinging it into the air, Misato yelled like there was no tomorrow in an effort to forget that brief flash of memory.

"AH! Yeah heheheh… I'm telling ya Shinji it's moments like these that make it all worthwhile don't you think?"

She noticed how apprehensive he still seemed. He sat with his arms crossed in front of him, his face twisted as if he were being held in the seat at gunpoint. Misato found she hated that look. It was as if he didn't want to be with her at all.

"Come on, Shinji. Live a little!" Misato told him. "You're not going to win over a lot of girls if you're just gonna sit there with an attitude. Make yourself comfortable!"

Shinji grimaced. "Yeah I guess so…"

He was retreating from her, lost in thought. A wave of indignation came through to Misato. She crossed her arms.

"Yeah, I guess so." Misato repeated with disdain. "You can't just agree with what everyone tells you!"

She aimed to grab his head, mostly as a joke. However, just before her hand could make contact, she caught him flinching and shutting his eyes. He was expecting to get hit, she realized in an instant. Ashamed of her slip up Misato merely rubbed his head instead. His soft brown hair between her fingers felt strangely nice.

"Well, this is your first day, so I can't be too harsh."

Shinji opened his eyes, letting out a sigh of relief. Misato could feel a crisis averted.

"Since you're done with food, why not take a hot bath? As Mom used to say, wash all those worries down the drain!"

He took her up on her offer at once, leaving for the bathroom. Misato still sat across the table, taking another can of beer into her lips. She was ever so slightly proud of herself for not offering a can to Shinji. It wouldn't set a good example to the kid if she broke a law right off the bat just to get him to live a little.

She didn't particularly enjoy having to be a good girl for anyone, but it couldn't be helped. Shinji needed guidance in his life, and no one else but her was willing to take up the task. Lord knows what would happen if Ritsuko tried to take him in. Or Kaji.

A shiver went down her spine at the thought of Kaji taking Shinji under his wing.

'I won't let that arrogant bastard sink his claws into my Shinji-kun!'

Such a perfectly well-behaved boy came once in a lifetime, Misato wasn't going to let anyone sully him. Not Kaji, not Ritsuko, not herself…

Huh. Misato realized she forgot to introduce Shinji to-

"AAAAAAAAAAHHH!"

Without warning, Shinji burst out of the bathroom door right where Misato could see him.

All of him.

Naked.

Misato didn't fight the blush forming in her face. She just listened to Shinji's pleas and warnings as she saw a penguin march out of the room. The penguin's smug aura snapped her back to reality.

"Um, yeah that was Pen-Pen…" She didn't like the small hesitation in her voice. "He likes to surprise people that way… so uh, you gonna go back in or are you happy to see me?"

Shinji seemed to realize he was in the buff. He flushed in embarrassment and tip-toed back inside the bath. Misato took another of sip her beer.

"Geez, first day here and I get to see him naked. I hope I didn't embarrass him too much."

The way his face reddened like a tomato was so cute, though. She was definitely going to tease him about this for years, assuming he elected to stay with her after the Angels were defeated. It'd be nice to have someone to go home to on lonely nights, pal around, get drunk with…

Misato blinked.

"Ugh, that's it. No more drinking for the night."

After he finished his bath, Misato took her turn. She allowed herself in the water, trying to shake the strange thoughts the alcohol brought out of her. Along the same lines, she decided to call Ritsuko and tell her about her ward's sudden move.

Ritsuko had plenty of fun at her expense.

"Yeah after all the horrible stuff he went through…" Misato said. "I don't think he'll pilot again."

"Maintaining him is part of your joooob…"

Misato wished she could teleport to Ritsuko and punch that unseen grin off her face, but alas, she was just a regular human being. Maybe if she had an AT Field like the Angels she could have amazing super powers like they do. It would beat relying on traumatized children to solve her problems.

"I'm just scared. He's my responsibility, but after Asuka I'm not sure if I'll be able to take care of him like I want to."

"It was your idea, so you pay the consequences. Besides, Asuka's probably more upset at you having dated Kaji than whatever happened in Berlin."

"Oh shut up!"

She didn't want to think about Kaji or Asuka. Not them.

"To be honest, I thought you'd be happier with the Angel dead. That's what you wanted, no?"

"You'd think, but I'm not." Misato shook her head. "You told me Unit 01 went berserk on its own. We saw how it killed the Angel with its bare hands. The Angel didn't even have time to pull a self-destruct. Shinji is already afraid of the Eva, who knows what else it could do?"

"Already a mother hen, Misato? We're triple checking the systems to ensure nothing like this happens again."

"You better see to that. I know Shinji can't leave, but that doesn't mean we have to make things harder on him."

"He has to grow up at some point, or we all die. I better get back to work. Good luck to your new roomie I guess, hope he doesn't run into Mr. Green."

Misato heard a click, staring at the phone in contempt. "Bitch."

She definitely needed to hide Mr. Green before Shinji came across that thing.

A few more minutes in the tub, Misato left the bathroom with a towel wrapped around herself. She was still soaking wet when she stopped next to a door. It was usually a guest room whenever Ritsuko or one of the techs came over for a drink. Now, it would be Shinji's room until the day he left her behind.

She narrowed her eyes.

"Ha, look at me. I rag on Ritsuko and the Commander, but I'm also treating Shinji like a tool."

She was thinking of him as a partner to relieve her loneliness. It wasn't what he deserved, and she was going to let him know that right now.

Keeping that in mind, Misato knocked on the door.

"Shinji?"

Not waiting for an answer, she slid the door open. She found Shinji, clad in a baggy shirt and shorts, laying on the side of his futon. His body was stiff, still as if he were asleep. Misato knew better. She could hear the uneven breathing coming from his nose.

Misato stepped closer to him. His body shifted, resigned to whatever she had to say as Shinji turned around to meet her. His eyes suddenly opened wide upon gazing at her still-wet, covered form. He said nothing as she placed her hand on his shoulder, causing him to blush and force his eyes away from the rest of his new guardian. It excited something in Misato, as she spoke:

"I know you didn't want to pilot the Eva. To be honest, I was worried about you the entire time you were fighting that Angel. Nothing I say can convey how proud of you I am for stepping up. For staying with me. I promise, even if I can't get you out of here I'll do everything I can to protect you."

Her eyes darted left to right, trying to think of something else to say. She sighed, realizing that she couldn't.

"Just… hang in there, okay?"

She said her piece. There was nothing more to be said.

Misato left Shinji alone, sliding the door shut behind her. Shinji moved his fingers the spot where she held him, feeling his shirt damp from the touch. He couldn't help but smile at her words.

"She is a kind person… I feel like I can trust her."

He laid his body back to the bed, plugging his earphones back into the SDAT player. He didn't want to think about the fight against the Angel, about the Eva and its monstrous form beneath the armor, about what he saw in his vision. He didn't want to think about anything.

"I hated that thing. I don't want to be here. I… I didn't do anything special or worth it."

In that respect, Shinji hoped Misato never got to see him for what the coward really was. He knew if she did, she would just be disappointed.

Author's Notes:

Gendo is going to eat his words, let me tell you.

Why is Mary Iscariot the Sub-Commander instead of Fuyutsuki? I might have an in-universe explanation later, but mostly I just wanted 1) a clear and obvious way to show this is an alternate universe and 2) do something a little different with Gendo.

It was admittedly a bit hard to power through the chapter when its pretty much the same as canon with minor deviations. I hope the subtle differences are interesting enough for you? Next time, expect more deviation from canon.