Shinji slowly drifts to consciousness and opens his eyes. Sleeping in a chair in the corner is his mother, Yui Ikari. The same Yui Ikari who had died in an experiment 12 years earlier.
'How? Am I dreaming? Is it really her?' Gendo walks in and walks to Shinji's side.
"You're awake."
"Yes. What is going on?"
"We're not sure."
"How is she here?"
"What do you mean?"
"Mom, how is she here? She died 12 years ago. YOU killed her, in an experiment."
"What experiment?"
"The first activation test of Unit-01. She was absorbed."
"Shinji... your mother was never involved in any activation tests. Not as a pilot anyway."
"I remember it though. I was there"
"... yes. You where. Your mother brought you to watch Mankind's greatest acheivement. The activation of an Evangelion. She's never forgiven herself for it."
"Why would she have to."
"I... I don't know how to say this, but the Eva went berserk. We evacuated the command center, but you wouldn't move. It smashed the glass and..."
"But... if that's true, how am I here? Why am I still alive?"
"That's our question too. Dr. Akagi will be here soon to perform some tests. Hopefully they will have some answers."
'Ritsuko...'

Dr. Akagi walks in and looks at Shinji.
'That is definately him. I would recognize his features anywhere....' "Good afternoon."
"Good afternoon, Doctor"
"If I could have some time alone with the patient, we can begin."
"Of course." Gendo lifts Yui and carries her out. Over his shoulder her eye opens. She spots Ritsuko as Gendo walks out the door.
"Well. Shinji. This is.... awkward. After what the Eva did... I was there that say. I saw it. I still see it."
"..."
"Right, anyway, let's get to business. I'm just going to need a few samples."
"Ritsuko."
"Yes?" Somehow it sounded natural coming from him, so she let it slide.
"Where is Misato?"
"Major Katsuragi is debriefing the remaining pilot."
"Pilot?"
"Yes, of the Evangelion."
"Only one?"
"Yes." Shinji's heart beats faster.
"... who?"
"Rei Ayanami, the first child." Shinji closes his eyes as he prepares to ask his next question.
"What about Asuka?"
"Who?"
"Asuka, Asuka Langley Sohryu, the second child."
"Oh, her. She's Nerv's German branch, I guess. I imagine she will be called over soon, to replace the third child."
"The third child?"
"Yes, a young man by the name of Touji."
"What.... what happened to him?"
"We don't know. He was absorbed into the Sea of Driac during the battle. The Eva had surely lost power, when it burst forth. We recovered it, but inside, we found... well... you."
"Then he's dead? Because of me?"
"We don't know that for certein. And he is replacable."
At the coldness of her voice, Shinji stops and cooperates with Ritsuko, to get her out as fast as possible.
'Replaceable. He was a human being, but all she can see is that he is "replacable".'

Yui and Gendo are out in the hallway during this exchange.
"It's really him, isn't it?"
"Yes."
"How can you be so sure?"
"Call it.... mother's intuition."
"You're a scientist, how can you believe that nonsense?"
"Science IS intuition. Coming up with a gut instinct and following through on it." Gendo smiles.
"You're right." Yui smiles.
"Of course I am, did you expect something different?"
"No. And that's why I love you so much."
"I love you too."
"I know." A brief pause.
"Gendo Honey?"
"Yes?"
"Put me down please."
"And if I don't want to?"
"Why, then I'll just have to kiss you into submission."
"Sounds horrible. Absolutely horrible."
"Oh it is."
"Let's try it, shall we?"
"Let's."

Ritsuko returns to her office and slumps into her chair. Shinji was alive. More than that, he appeared to be fully normal, exactly as the records showed he should be. She was, in short, astounded. Misato walks in, grabs a cup of coffee and looks at Ritsuko's monitor.
"Who's that."
"Shinji Ikari, Yui and Gendo's son."
"I heard about that, the activation experiment of Unit-01. Very sad."
"It was. They were both were complete wrecks for months, neither of them were able to function."
'Ritsuko can never see the human side of it...' "Why are you looking at his records?"
"Something very strange has happened. The strange boy who emerged from the entry plug appears to be him."
"What are you talking about?"
"He has identical DNA, and both parents are firmly convinced it's him."
"You're not so sure."
"No. It violates every law of science we know of."
"But I'm sure science has an explination."
"That's what I'm trying to find. Unfortunately, nothing is forthcoming."
"You'll figure it out."
"I hope so."

Shinji is released from the hospital and moves in with his parents. He begins to learn the differences in this world. Gendo and Proffessor Fuyutski are reversed, and Yui is alive. Asuka is still in Germany. Touji was the third child. It all looked the same, but... it FELT different.
'What's happening? Why is everything so different?'
"Hey, new boy!" Shinji has started school.
"Yes?"
"Where's Touji. He disappeared in the last fight, and then you show up. What's going on?"
"I.. I'm not sure myself." 'Why is Kensuke acting like this?'
"*hmph*, I'm sure you don't."
"I really don't. Look, why don't we be friends? My name is Shinji Ikari."
"Ikari? Now I really don't believe you. You're the subcommander's, not to mention the head of Project-E's son."
"... Yes."
"Whatever they're doing, tell them to stop. I want my friend back."
"y... yes." Kensuke walks away
'Why on Earth was he acting like that? Kensuke's nothing like that normally.'

Rei looks over at her brother. He is staring off into space while the teacher drones about the nuances of pre-third impact life. She smiles to herself.
'He's fitting in already.' After the bell, she walks over to him.
"Hello, brother."
"Brother? What do you mean Rei?"
"Well, you're my brother! What else would I mean?"
"You're.... my sister. I have a sister?"
"They haven't told you yet? Then how did you know my name?"
"Nevermind. You're my sister." He stands up and hugs her.
'Well, I take it he likes the idea.' She hugs him back.
"I love you, Rei."