Everything to do with Eva doesn't belong to me, it belongs to Gainax
After the last episode some of you may be wondering, what the hell is this guy thinking? If only you knew. I have something to say, I have seen End of Eva, class film, that's where I got the inspiration for the Gendo and Shinji storyline. After seeing that film I honestly believe that Gendo loves his son. Thoughts are in and actions/events are in ().
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Neon Genesis Evangelion: True Destiny

Episode 14 The Investigation/Letters
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Touji stepped away and let the medic do his job, he felt for a pulse, but he couldn't find it, they tried shocking Shinjis heart, but it did no good.

Medic: I'm sorry, but he's dead.

Yui: What...

She fainted. Asuka looked at Shinjis body and ran off, Touji ran after her, Misato stood there for a second, shouted a few orders, and then started crying, she collapsed to the floor, and beat her fists on Unit 01s back. Touji caught up with Asuka, grabbed her hand and pulled her into an embrace, she was also crying uncontrollably, a few tears ran down Toujis cheek.
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The next day, in the briefing room are Fuyutsuki, Ibuki, Aoba and Hyuga, all of them look like they have at least shed a tear.

Fuyutsuki: Commander Ikari, Dr Ikari and Major Katsuragi are taking a few days off, so I'll be in charge until their return. I know that this is an emotional time for everyone but we have a job to do, and I want it done before the Commander returns. Right first I want the status of all the Eva Units.

Ibuki: Unit 01 sustained damage only to the area of the armour where the Lance penetrated, there is no other damage. Both of Unit 02s arms were broken it will take a week to repair it. Unit 11 has been completely destroyed, there is no chance of recovery.

Fuyutsuki: And Unit 04?

Ibuki: Unit 04 is fully operational. It has been completely silent since yesterday, it has been stored in the 10th cage as per your orders.

Fuyutsuki: Right, I want Unit 02 repaired as fast as possible and I want Unit 04 analysed from top to bottom, if the analysis proves without a doubt that there is no contamination, then I want the fourth child to be its designated pilot, make sure that it is ready for him.

Ibuki: Yes sir. But I don't know if he will pilot it.

Fuyutsuki: I'm sure he will, eventually. By the way, do we have any idea of why Unit 04 destroyed its entry plug or even how it was able to do so?

Aoba: I never noticed it during the battle, I'm afraid I was too concerned over Unit 01, but the MAGI detected a blue pattern when the plug was ejected. After analysis the MAGI confirmed that the pattern was identical to the 17th Angel, I believe that the plug was a dummy plug based on the 17th Angel similar to the ones used in the mass production Eva's. Further analysis of the remains should confirm this.

Fuyutsuki: A dummy plug? I knew that Unit 04 was going to be using one, but I though that it was going to be one of ours, not one of SEELEs. Lieutenant Ibuki, if memory serves me correctly I believe that according to the timetable, when Americas second branch disappeared, that they were installing and testing the S2 engine, not activating the Eva.

Ibuki: I searched our files and the files recovered from SEELE, apparently the copy of the timetable we were given was a day behind.

Fuyutsuki: SEELE didn't want us to know that they were using a different dummy plug. Is the appearance of Unit 04 related to the explosion detected in space yesterday morning?

Hyuga: After discussions with several observatories around the world, we now know it was. Debris at the area has been identified as the Second branch. No word from the Americans though, it seems that they cut off all communications before the incident, they probably don't know what happened.

Fuyutsuki: Right, now do we have a cause of death for Shinji Ikari?

There was a short silence.

Ibuki: The report states that he died from massive blood loss from wounds on his hands, feet and abdomen, the report is unclear on how he received those wounds.

Fuyutsuki: He got those wounds from contact with the Lance, no one believed that such a thing could be possible. That's all for now, dismissed.

Silently the bridge officers left the briefing room, several minutes later Fuyutsuki did too.
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Three days after the incident, Touji is at the door to the apartment that Shinji shared with his mother, he rings the bell. To his surprise, Commander Ikari answers the door.

Ikari: Mr Suzahara, what can I do for you?

Touji: C..C..Commander Ikari! Erm...These are for you and Mrs Ikari.

He hands the Commander two envelopes.

Touji: Shinji wrote them for you.

Ikari: Thank you Mr Suzahara, goodbye.

Touji: Goodbye Commander.

Touji walked away and Ikari shut the door. He went through the house to his wife's bedroom.

Yui: Who was it?

Ikari: It was Touji Suzahara.

Yui: What did he want?

Ikari: To give us these, letters from Shinji.

Yui started crying, Ikari held her.
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Meanwhile Touji had walked next door and had rung the doorbell on Misatos apartment. Misato opened the door.

Touji: Hey Misato, how're you doing?

Misato: Getting there, you?

Touji: Same, how's Asuka?

Misato: She's taking it as hard as Yui, I can't believe how the Commander has been, he hasn't left her since they got there, he's been sleeping in Shinjis rooms though.

Touji: Anyway I have to give you these.

He hands her two envelopes.

Misato: What are these?

Touji: Letters from Shinji, he asked me to make sure that everyone got them.

Misato: Letters from Shinji, thanks for bringing them over.

Touji: No problem, say hi to Asuka for me.

Misato: So what are you going to do know?

Touji: I have to tell Hikari and Kensuke about Shinji, I just haven't found the right words to say it. Then I have to go to headquarters for tests.

Misato: Are you sure about the tests?

Touji: Shinji wrote a letter to me, I've already read it, it helped.

Misato hugged Touji.

Misato: Okay, I'll see you later.

Touji: Yeah, bye Misato.

Misato watch Touji walk away and then closed the door. She walked into Asukas room.

Misato: Hey Asuka.

She sat down on the bed. Asuka, who had her back to the door, rolled over and grabbed Misatos waist. Misato lay down on the bed and wrapped an arm around the girl.

Misato: Asuka, this is for you, it's a letter from Shinji.

The girl looked up.
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Hikari and Kensuke meet up outside Toujis place.

Hikari: Hey Kensuke, do you know what is going on?

Kensuke: No, I've called Touji and Shinji for the past four days, there's been no answer.

Hikari: The same with Asuka, I wonder what happened.

They rang Toujis doorbell. Touji answered the door, he looked drained.

Hikari: Touji are you all right?

Kensuke: Yeah man, there hasn't been a word form you or Shinji since the last battle.

Touji: I'm sorry I didn't tell you guys earlier, but I was busy.

Hikari: Tell us what?

Touji: Shinji..Shinji's dead.

Hikari: What?

Kensuke: It can't be true.

Touji: It is, here these are for you.

He hands them an envelope each. Hikari had started crying, so had Kensuke.

Touji: They're from Shinji.

Hikari: Asuka, how is she?

Touji: She's taking it really bad. You should go see her.

Hikari put her arms around her boyfriend.
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Later that night everyone read their letter, some for the first time, some for the twentieth.
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Hikaris Letter

Dear Hikari

I know that we aren't the best of friends,
we only hung out on a few occasions, but I
do consider you to be a good person, and
someone that I could possible turn to. I
only hope that you feel the same way about
me. I am writing this letter to tell you
how I feel about you and what I would like
you to do, I have already told you how I
feel about you so all that's left is to
tell you what I'd like you to do. Watch
over Asuka, Touji and Kensuke for me, they
will need someone like you, someone who is
strong and caring. I know that you will
probably do it anyway, but I want you to
know that I wanted you to do this for me.

Thanks
Shinji
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Kensukes Letter

Dear Kensuke

Hey, how are you doing? If you are
reading this then I am dead, probably
killed in battle. I know we already
discussed this, but this is the result of
war, death. I know what you have been up
to recently, Touji hasn't got a clue
though, keep at it, I know that you will
be great if you continue in that line of
work, but then maybe you have always been
that way, just remember to conserve a
persons privacy and report the facts. I
read the article you wrote, I can't
believe that you were published. How did
I know that? I have my sources, namely
Misato, but she only told me. You should
write about me, I want you to. If there
is an afterlife, I'll see you later.

Shinji
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Toujis Letter

Dear Touji

If you are reading this then thank you for
delivering all the letters. Thanks also
for being a friend, for forgiving me for
what happened to you and your sister. I
have a little confession to make, do you
remember when you told me and Kensuke that
an anonymous someone had paid all of Maris
medical bills? That was me, although you
probably guessed that, it was the least
that I could do. I have one last favour
to ask of you, look after Asuka, do
anything that you have to, to look after
her until she is ready, even if that means
doing something that you don't want to do,
it would mean a great deal to me.

Your friend
Shinji
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Ikaris Letter

Dear Father

Lately we have been getting closer to what
could be called a true father/son
relationship, I'm glad. You have done a
lot of unforgivable things, and I know the
reason behind them, I suppose that I
should never forgive you, but you have
been trying, what you did for Asuka was
one of the good things that you have done.
Our recent talks have been interesting, I
have also been talking to Mom. I know for
sure that what you did, you did for our
family, now all you have to do is piece
our family back together again. Mom still
loves you, and you are my father, what I
want to say is, that now I'm gone I want
you two to be happy and I know that means
for you two to be together again. You
know what father, when I wrote this letter
I had decided that I could never forgive
you for a few things, but I have forgiven
you for a lot of things, and I had decided to
put those last remaining things aside, to
give our family a chance. Until we meet
again.

Your son
Shinji
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Misatos Letter

Dear Misato

First off I want to thank you Misato, what
you have done for me ever since I came to
Tokyo-3 can never be repaid. You were a
mother or a sister or a friend whenever
I needed one. I know that you were upset
when I moved in with my mother, I was
upset in some way too, I miss the days of
living with two women who would constantly
tease me with their flimsy clothes. How
many times did you and Asuka come out of
shower holding the towel loosely? I want
to say that I am proud of you, I have
noticed recently that you haven't been
drinking as much, although Pen Pen has
been rather upset with you. I miss Kaji,
I think you two were good for one another,
I hope that one day you will find someone
as good as him. There is one last thing
that I want you to know Misato, after all
this time I know that I love you, and I
don't know what I would have done without
you.

Love
Shinji
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Yuis Letter

Dear Mother

Our time together is always short, we have
just gotten to know each other and now we
are separated again. There is so much
that I have to say, so much that we have
to make up for, but we can't, so I have
left this letter. We have discussed a
lot of things, the past, the present and
possible futures, but the only question
that I have always wanted to know was: Do
you love me? When you returned, I knew
that answer as soon as you held me, and I
know that you know that I love you too.
Saying this, there is something I want you
to do, I want you to be happy, and that
means being with father. He and I have
been getting closer lately, I am beginning
to feel that we are truly father and son.
I want you to be with him, if you want to
be with him. I know you still love him,
and that he still loves you. I want this
to happen.

Love
Shinji
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Asukas Letter

Dear Asuka

When I wrote this, you didn't want to
speak to me, I know some of the reasons
why, but not all. I wanted to know you,
to be with you, but now I'm gone. I had
planned to speak with you, hopefully I
have, but if I haven't then here is what I
have to say. I love you Asuka, ever since
that Angel showed me who I wanted to be
with I have known for sure, yet I have
suspected it for a long time, I know that
you are hurting inside, that you have been
hurting for a long time. I was once told
that without a definition of pain, I can't
define happiness, I have been through a
lot of pain, as have you, and I have come
to realise that my definition of happiness
is you. I want you to never forget me,
and I want you to move on. Let go of the
past and look to the future, I'm
depending on you.

Love always
Shinji
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Asuka had read the letter for the fifth time, she wasn't ready to let go of him just yet, but she was ready to let go of a few things that she still held on to. She had been crying for a while now, and she still cried until she fell asleep.

To be continued...
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I want to make sure one thing is clear, Shinji is dead. I won't do a 'Death of One' thing either. But how am I going to explain all the questions that have been on every ones lips? You have to wait and see.