Everything to do with Eva doesn't belong to me, it belongs to Gainax
By the end of this chapter you should be able to predict what is going to happen in the next chapter. I'm happy with the way this is progressing, and I hope to update the first few chapters soon, there are a few scenes that I would like to add. I would be greatfull if someone who didn't like the story, or what's happening, told me what was wrong so I could fix it, I feel like I walking in the dark. Anyway onto the story. Thoughts are in and actions/events are in ().
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Neon Genesis Evangelion: True Destiny

Episode 5 Regeneration
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Shinji could not believe his eyes, standing before him was Touji Suzahara, in shorts and t-shirt. He was actually standing, all limbs present and accounted for.

Touji: Shinji.

Shinji: Wha...How...Who...??

Touji: I'm sorry, but I asked your mom not to tell you about this.

Shinji: Huh?

Touji: I've got my arm leg back and all you can say is 'huh'.

Shinji: That's great! Unbelievable! What's going on?

Touji: About two weeks ago your mother came to see me.

Flashback

Two weeks ago. Touji is lying on his hospital bed, when there is suddenly a knock on the door.

Touji: Come in!

Yui Ikari walks through the door, Touji is surprised to see her. He feels a little awkward around her, since Shinji had explained everything about Rei.

Touji: Mrs Ikari, what can I do for you?

Yui: It's not what you can do for me, but what I can do for you.

Touji: Excuse me.

Yui: How would you like your life back? Because I can give it back you know.

Touji: You mean...

Yui: Yes.

Touji: What's the catch?

Yui: I'm sorry, I don't understand.

Touji: NERV always wants something in return for services.

Yui: I assure you, I want nothing in return, this is for Shinji and for me, we both feel guilty about what happened, and I have to make it right.

Touji looks into her eyes, he can see she is telling him the truth.

Touji: Okay then, lets get out of here.

End Flashback

Touji: So then she took me to this lab, under headquarters, there was a big glass tube down there, she stuck me in it, a few days later I was whole again.

Shinji: Then where have you been since then.

Touji: Here, undergoing physical therapy, I just had my first run, I thought you had gone home already. You were supposed to find out at dinner tonight.

Shinji: I wondered why mom was curious about dinner, she never usually is.

Touji: Misato knows as well, I'm going to be staying at her place until the residential block is completed.

Shinji: Aren't you going to tell Hikari and Kensuke about this? They've been worried about you.

Touji: I'm not supposed to tell anyone, at least until the public announcement.

Shinji: There's going to be a public announcement?

Touji: Yeah. Your dad thinks that this will improve NERVs public image. I'm surprised you haven't been told about it. I thought that they were going to parade you around as the saviour of the world.

Shinji: I wish people would let that go.

Touji: At least you haven't completely changed.

Shinji: Sorry?

Touji: You still don't like people making a fuss over you.

Shinji: Yeah. Come on lets go mom and Misato are waiting for us. But first I have to go see Asuka.

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In Brussels, a special meeting of the UN council has been called to discuss the future of NERV. The council is made up of representatives of each member country of the UN.

Japan: I say that NERV should continue, the Japanese Government are willing to declare Tokyo-3 as an independent state, where the UN council should relocate to. The Geofront is the perfect place, to aid in peace treaties, especially with the Evangelions defending the city.

America: The US government is clear on where we stand. NERV should be disbanded and all materials relating to the Evangelions should be destroyed.

France: I agree with the Japanese representative, but NERV should only exist in Japan and operate under the direct control of the UN council. The Evangelions are great weapons, far more lethal than an N2 mine, they could aid in border disputes with non-UN countries.

America: Irrelevant, they pose a threat to the US.

Britain: Why are you so scared of the Evangelions? I think that most people agree with the suggestion made by the Japanese representative, Tokyo-3 shall become the capital of the UN, all in favour raise your hand.

All representatives, except the US rep, raise their hands.

Britain: All those against.

Only the solitary hand of the US rep rises.

Britain: Motion carried.
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At the 6th Cage, Unit 11 stands. Two people are standing in front of it, Commander Ikari and his wife Yui.

Ikari: What is the status of Unit 11?

Yui: There was only damage around the entry plug area. It has been repaired, analysis of the core, reveals that a personality hasn't been imprinted on it. It is safe to use.

Ikari: And Unit 10?

Yui: The head and the top of the spinal column were completely destroyed, there is no chance of repair, the S2 engine is in perfect working order though, I suggest that it be installed in Unit 02.

Ikari: Fine, what of its core?

Yui: It's core is fine.

Ikari: Dispose of the remains of Unit 10, including it's core.

Yui: Fine.

Ikari turns to Yui.

Ikari: Yui...

Yui: Gendo, we have discussed this.

She looks at his right arm.

Yui: I hope you now feel what it's like to be a guinea pig.
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Shinji and Touji are walking to the hospital, Shinji can't help but stare at Touji's leg and arm, he noticed that Touji was limping slightly.

Shinji: Touji, why are you limping?

Touji: My new leg is as strong as my other one, but its getting there. I still can't believe how much you've changed.

Shinji: Me either, I do things, and later I wonder how I did them, I would never have done them before.

Touji: Will you tell what happened?

Shinji: I'm sorry Touji, I can't. If anyone were to find out, alot of people would get hurt.

Touji: I won't tell a soul.

Shinji: It's not you I'm worried about, it's them.

Touji: Who are 'them'?

Shinji: NERV security, I'm not supposed to be followed in the Geofront, but sometimes I'm not too sure.

Touji: Oh, I see.

Touji looked around, he thought he saw someone behind some bushes, but he wasn't sure.

Shinji: You get used to it.

Touji: I don't know if I could.

Shinji: Well, if you think about it, when we hung out together, NERV security was always there.

Touji: What! Even that time...

Shinji: Yeah.

Touji: Oh, so that's why you didn't want to do that.

Shinji: Yeah.
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They arrive at the hospital, and go directly to Asuka's room. Touji was stared at by most of the doctors and nurses who worked there. They arrived at Asuka's room to find that Hikari and Kensuke had left long ago.

Shinji: I'd better go in alone.

Touji: Yeah sure, actually while I'm here I may as well visit my sister. I'll meet you at the entrance in half an hour.

Shinji: Okay, see you then.

Shinji walked into Asuka's room, he notices that she had been crying.

Shinji: Asuka, are you alright?

Shinji walked over to the bed and sat down beside her.

Shinji: Asuka, tell me what's wrong.

Asuka: I thought you weren't coming back.

Shinji: I'm sorry, I promised you I wouldn't leave you, but something has happened.

Asuka: What?

Shinji: Touji, my mom was able to restore his arm and leg. It took me by surprise.

Asuka: Oh.

Shinji: Don't be upset, I'm sorry I couldn't spend as much time with you today as I wanted to, I'm afraid that I won't be able to spend as much time with you as I have been, now that testing has resumed on Unit 01, but I will try. Feeling better?

Asuka: A little. Thanks.

Shinji: No problem, well I'll see you tomorrow, goodnight.

He lightly kissed her on the forehead, and then left. Shortly afterwords Asuka fell asleep, smiling.
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Shinji: Mom, I don't think you cooked enough.

Back at the apartment, Shinji was talking to his mother about dinner.

Yui: Why? There's more than enough for the five of us.

Shinji: Just goes to show that you don't know Touji very well. His nickname is 'The Stomach'.

Yui: 'The Stomach'?

Shinji: Yeah.

Yui: I suppose I could make more rice.

Shinji: Here, I'll help.

Yui: Oh no you don't, go speak with your friend.

Shinji: He's too busy drooling over Misato.

Yui: Well then tell me, who is this Penpen?

Shinji: He's in the bath at the moment, he'll be out in a minute.

Yui: But he's been in the bath ever since I got here.

Shinji: Yeah, we have a hard time getting him out of it.

Suddenly they heard the bathroom door open, and Penpen walked past them, heading to his fridge. He stopped and look at them.

Penpen: Warrgh.

Shinji waved to him, then he continued to his fridge, Yui looked on in disbelief.

Yui: That was a...

Shinji: Yeah.

Yui: But how?

Shinji: He's a warm water penguin.

Yui: Warm water penguin? I remember hearing something about that project.

Soon dinner was ready and the four of them ate and more embarrassing stories were told about Shinji. He was getting used to it now, but he wondered why they only talked about him. After dinner, Touji and Shinji played video games, while Misato and Yui discussed the future of NERV. Touji stayed the night at Misato's in Shinji old room, he was going to stay there until the residential block was built. Needless to say, Touji was a very happy young man.
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Two more weeks passed. Asuka had started walking again, and the doctors had allowed her to go home. So Misato helped the girl back to the apartment.

Asuka: Misato, where's Shinji?

Misato: He's probably at home.

Asuka: But we are home.

Misato: Oh, he didn't tell you.

Asuka: Tell me what?

Just then Touji walks in from the bathroom.

Touji: Hey guys, how's it going?

Asuka: What's he doing here?

Touji: I live here.

Asuka: WHAT!

Misato: It's only a temporary arrangement, until the residential block is finished.

Asuka: So where's Shinji?

Touji: Why do you care where Shinji is?

Asuka: NONE OF YOUR GODDAMN BUSINESS!

Misato: Looks like she's almost back to normal Calm down Asuka, Shinji moved out of here and in with his mother.

Asuka: Why didn't he tell me?

Touji: Because it's only next door. He still cooks for Misato and me, damn he's almost as good as Hikari.

Misato: So you like Hikari eh? What about me?

Touji turned red, and took a page out of the old Shinji's book. He ran.

Misato: Boy's are so easy.

Shinji: Is that so.

Misato: AAAAHH!!. Why the hell did you scare me like that?

Shinji: To prove that women are as easy as guys.

Misato: Damn instrumentality

Shinji: Hi Asuka, I'm sorry that I didn't tell you about me moving in with my mom. So much has happened over the last month.

Misato: Tell me about it.

Shinji: It is quite exciting though. The UN council being relocated here, and Tokyo-3 being declared independant of Japan. We're going to be governed by the UN council.

Misato: As the only Eva pilot, you have a great responsibility, to protect this city from all attack.

Shinji: I'm honoured to do it.

Misato: That reminds me, we have a meeting with the UN council tomorrow, just you and me.

Shinji: The UN council?

Misato: Yeah, they want to meet the heroic pilot of Unit 01.

Shinji: Not again.

Misato: This is part of your job now.

Shinji: I know, doesn't mean I have to like it.
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Later on, Shinji says his goodnights to Misato, Asuka, Touji and Penpen, and walks next door to his own home. His mother shouts to him from the kitchen.

Yui: Shinji? Is that you?

Shinji: Yeah mom.

Yui: How's Asuka?

Shinji: Fine, just settling back in.

His mother walks in to the living room.

Yui: Shinji, I have something important to tell you.

Shinji: What?

Yui: We have finished repairs on Unit 11, and finished installing an S2 engine into Unit 02.

Shinji: Excuse me? But I thought I destroyed all the production Evas?

Yui: Not exactly, you destroyed Unit 11s entry plug and Unit 10s head and entry plug, Unit 11 only needed a little repair and Unit 10s S2 engine was still viable.

Shinji: So who are you getting to pilot them?

Yui: That's the thing, we need to test them to make sure that the work with another pilot first.

Shinji: You mean me.

Yui: Yes. Will you please do it?

Shinji: Okay I'll do it, but only because you asked me nicely.
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Shinji is now standing in front of Unit 02, he is standing in his plugsuit, and his mother is walking up to him.

Yui: Hey Shinji how are you doing?

Shinji: Alright.

Yui: Okay then, we're going to start with Unit 02 and then move on to Unit 11.
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Warning signs appear on the monitors.

Yui: It's no use, Unit 02 is just not going to accept another pilot, I wonder if...

Ibuki: Ma'am?

Yui: It's nothing Maya. Eject the plug, and shut the system down.

Ibuki: Yes ma'am.

Yui: (Into Microphone) Shinji, we are now going to try you in Unit 11, so could you move to the 6th cage.

Shinji: (Over Comm) Yeah mom.

A few minutes later.

Ibuki: The pilot has reached the entry plug. He has entered and is awaiting entry.

Yui: Inject the entry plug into Unit 11.

Ibuki: Injecting plug.

Yui: Activate the Eva.

Ibuki: First stage connections are completed. Second stage connections are completed. Commencing third stage connections, 1.9 to absolute borderline, 1.7, 1.3, 1.1, 0.9, 0.7, 0.5, 0.4, 0.3, 0.2, 0.1 borderline clear the Eva has been activated.

Yui: What is the synch ratio?

Ibuki: It's odd it's holding at 3%.

Yui: That's fine, considering that there is no personality matrix in the core yet, in fact its higher than I thought it would be. Okay Shinji we're done here.
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Two more weeks pass, and the residential block is now finished. The families of NERV personnel move back to Tokyo-3, among them are the Horaki's and Kensuke. Touji has also moved out of Misato's much to his displeasure, and has moved into his families new home. He wonders why his family didn't want a place in Misato's apartment block, since all but two apartments were vacant.
Then he remembers his dad saying something about not wanting to live near two of the highest ranking members of NERV.

Touji: That is a stupid reason.

Yui: Hello Touji.

Touji: Oh Mrs Ikari what are you doing here?

Yui: I have come to ask you to consider something.

Touji: What?

To be continued...