Disclaimer: I don't own Evangelion. Gainax does. If they ask, I'll
delete this story from the Internet and my computer.
[This is thought]
"This is speech."
Evangelion: Child of Desperation
Chapter One: Dark Secrets
A Richter Scale Production
"Sub-Commander Fuyutsuki," the secretary called over the intercom, "Pilot
Ikari is here to see you."
"It's time," the aged man muttered. Reaching down to the call button, he
said, "Send him in."
Footsteps were heard outside as a fifteen-year-old boy approached the oaken
door of Sub-Commander Fuyutsuki. "Y-You wanted t-to see me, sir?" Shinji
Ikari stuttered as he entered the chamber.
"Yes, I did. Come," said the old man as he gestured to a chair, "sit down.
We have much to discuss."
The timid young man made his way to the leather chair that the Sub-
Commander pointed to, a far cry from the hardwood chairs in his father's
office. As Shinji sat down, he immediately began to look at his feet, like
a child who was caught with their hands in the cookie jar.
"Shinji," the old man began, "how are things at home?" The old professor
knew that the Katsuragi residence had become a real home for the young
Ikari and Pilot Sohryu. He also knew that things had become more strained
there since the 12th Angel. Asuka's insults towards Shinji had become
steadily more brutal, and Major Misato Katsuragi's absence from the
apartment only added to the stress.
"Fine, sir," Shinji said. "Asuka is a little tense, and Misato's been gone
since the night she got a strange message on the answering machine. I
think I'm coming to terms with my 'absence'." Absence! Hah! More like
nonexistence. The crew still doesn't know how this young man came back
from Unit 01. "Sir, is this why you called me here?"
"No, Shinji. I've called you here for a different reason. I was just
curious how your home life has been recently." Fuyutsuki took a few
moments to collect his thoughts before he continued. "Shinji, it has come
to my attention that you've been looking into your father. May I ask why?"
"Well sir," the young Ikari began, "I want to know just why he left me
after mom died. I've never gotten a straight answer from him."
"Do you really want to know, Shinji?" the old professor said hesitantly.
"I could tell you, but it may make things worse. You may feel worse than
ever after I tell you. So I'll ask again, 'Do you really want to know?'"
He tensed a little as he waited for Shinji's answer.
Shinji thought about it for a minute before coming to a decision. [It
might be painful, but if I can understand my father a little, it may be
worth the pain.] "I'm sure, sir. I want, no, need to know why I was left
behind for so long."
"Alright, Shinji. I'll tell you." Fuyutsuki pressed a few buttons to turn
off the surveillance equipment before beginning. "It all began about
fourteen years ago. I had just learned about the marriage between your
mother and father and of your birth. I never really took Gendo for a
family man, but Yui once told me that she wanted one. They dated since a
couple years before Second Impact, and I had heard that things were a
little shaky before . . . that day. After I came back to Kyoto, I
approached Gendo with some information linking him to Second Impact."
"What kind of information?" Shinji interrupted.
"Basically information that indicated that he not only knew Adam would
awaken, but he may have helped orchestrate Second Impact," Fuyutsuki
continued as he turned his chair around so that he faced the wall behind
his desk. "Anyway, he brought me into Project E, where I was reunited with
your mother. Yui happened to be the head of it.
"About two weeks after I started work on Project E, your mother asked to
meet her in a nearby park that afternoon. I waited a half hour before she
arrived. As she approached me, I noticed a large bruise across her left
cheek. When I asked her where it came from, she had told me that that was
what she needed to speak to me about."
*************BEGIN NARRATED FLASHBACK***************
"Yui! What happened to you?"
"Professor, I don't know what to do! I'm so afraid!" She wept, Shinji. I
hadn't seen her cry before, and it scared me.
"It's alright, Yui," I said as I drew her in for an encouraging embrace.
"Whatever it is, I'm sure Gendo and I can handle it."
"No, that's just it. Gendo is what's wrong!"
"Yui, try to calm down." It took a couple of minutes for her to calm down
before I could continue. "Now, tell me exactly what's the matter. You can
trust me, remember?"
She started slowly with a calm voice, "It all began about three months
before the incident. I had found out that he was cheating on me with my
good friend Naoko Akagi. She told me about it one day. I didn't believe
it at first, but she showed me the ring I gave him. HE told me it fell in
the sink!" she yelled. I could tell that it troubled her, but I knew that
she wanted to tell me everything. "I couldn't blame her for it, though. I
knew that she was attracted to him, but I thought that Gendo was faithful.
That evening, I made my decision to break up with Gendo Rokubungi. I was
going to do it the next day, when he was to take me to dinner.
"The evening started out like usual. He took me to the most expensive
restaurant he could afford, which was always surprisingly good. We talked
a bit about trivial things; he kept asking more about the committee while I
tried to talk about family. I knew it would normally get him to stop
asking questions, but that night, he just kept going.
"Before I knew it, we were leaving the restaurant, yelling at each other.
He kept telling me that I was dumb for thinking about starting a family,"
she grimaced as she spoke. "I kept saying that I wasn't being foolish for
wanting a family and that I knew about his other activities. Suddenly, he
hit me." That angered me, Shinji. The image of anyone hitting Yui was
like a blow to my soul. I flinched as she continued telling me of her
experience, "He just backhanded me to the ground. I finally shouted to him
that we were through. I guess I should have waited till I got home before
I broke the news to him.
"Gendo was enraged. He slapped me some more before he pushed me into his
car. I think I hit my head on the dash, because the next thing I remember
was waking up in his car. He parked it up on that hill. You remember,
Professor, the one you and I hiked up when I first told you I was dating
him. That bastard inched his way closer to me. I tried to escape, but the
door was locked. I couldn't unlock it because only the driver's side door
could be unlocked from the inside.
"As he got closer, I tried to fight back, but he somehow tied my hands
together. Kicking him was no good, since he grabbed my legs and pinned
them. He tore my clothes, and then he . . . he . . . he RAPED ME!" she
finally cried as she wept on my shoulder. Her tears were all that kept me
from immediately rushing to rip Gendo into more pieces than when Unit 01
broke out of the 12th. Yui must have picked up my increasing rage towards
Gendo and tried to calm me.
"Professor, there's more," she said hesitantly. She may have thought that
I had calmed, but in truth, I had just pushed back my anger so I could help
her. "I had hidden myself from everyone for two weeks after when I noticed
that I missed my period. I was frightened, Professor. It took a lot of
convincing from Naoko, whom I'd already told about the incident, for me to
finally check with my doctor.
"For another week and a half, I tried to resume a normal life while
worrying about the possibility of being pregnant. Imagine me, the one who
always wanted a family, afraid to have a baby. I couldn't kill an unborn
child, even if it was HIS. I made sure to keep my distance from Gendo, and
Naoko was careful not to mention HIM around me.
"Finally, the doctor gave me the news. Unfortunately, I wasn't alone in
hearing the news. The doctor thought that it was important to not only
inform the mother, but the father and grandparents-to-be. My parents were
distressed that I was unwed and pregnant; they didn't even listen to me as
I told them how I got pregnant. I couldn't believe it when they said that
I would marry Gendo, the man who raped me. There was no way I could argue
with those stubborn fools, so I made a concession. If I had to marry
Gendo, I was not going to take his name. My parents objected, of course,
but he agreed to take my name.
"A month after Second Impact, Gendo and I became Mr. & Mrs. Gendo Ikari. I
hated the idea of being his wife, but at least I managed to keep him far
away from me on our wedding night. We kept our distance until my son was
born in June of 2001.
"I started work on Project E, which Gendo promoted to the committee. I
managed to convince Naoko and another friend, Kyoko Zeppelin Sohryu, to
help with it. It was easy to convince Naoko to help as I insisted that it
was the perfect way to prove her Magi theorems. Kyoko was another matter.
She was expecting her daughter, Asuka, in December 2000, and she getting
ready to move to Germany with her husband Alfred. I told her that she
could take time for her daughter if she wanted and that if the project is
approved, she could have her own research staff in Germany. That was
enough to make her agree to join, as she never had her very own research
staff for a project.
"I was worried on the day Shinji was born. A thousand questions filled my
head as I went into labor. Would he look like his father? How much like
his father will he be like? How will Gendo look at Shinji? These
questions kept repeating itself as the doctors told me to push. Gendo was
in the waiting room, obviously trying to hide from me. He knew that if he
approached me, he would probably loose a couple organs. Five hours later,
I held my son for the first time. I had considered putting little Shinji
up for adoption earlier, but those thoughts went out the window as I held
him. He looked so peaceful, so innocent, and so beautiful as he slept that
I decided to raise him as best as I could.
"Gendo came in a few minutes later and asked to see Shinji. I guess that
in the euphoria of holding my baby, I agreed to let him see Shinji. Gendo
was the father and my husband after all, so he had the right to see the
child. Shinji shifted a little as Gendo held him in his arms. I could
swear that the expression on Gendo's face softened a little as he held baby
Shinji in his arms. As Gendo gave the baby back to me, Shinji's eyes
opened, and he smiled at both of us. It was so beautiful.
"After that day, I wondered if Shinji's presence could change Gendo for the
better. I'll never forgive him for what he did to me, but maybe Gendo
could be a better man with Shinji's help. If he could, then I might learn
to love him.
"A few months after Shinji's birth, I noticed that Gendo had changed.
There are times where he'll be kind and gentle, particularly when Shinji's
in his arms. However, there are also other times where he's violent,
particularly when I'm paying more attention to Shinji than to the project.
I don't know what's wrong with him, Professor."
"It's okay, Yui. I'll do what I can," I said. It was more like; "I'll do
what I can to keep myself from killing that fucking bastard." I couldn't
say that to her though. She needed a shoulder to cry on, and I was the one
to give her that shoulder.
I couldn't believe it. She was hoping that your father would change. She
didn't know it, but your mother was still in love with Gendo, or at least a
side of him. Over the next couple years, your mother came to the
realization that he'd never change. As she realized that, the part of her
that still loved Gendo died.
Then came the day of that accident. You may not remember it, Shinji, but
you were there. Your mother told me that morning that she was going to
divorce your father. She'd inform him after she would refuse to test Unit
01. Yui told me, however, that she would allow joint custody of Shinji
with him. I guess she still had hopes that you could influence him.
We didn't know that Gendo brought you with him until we arrived at the test
site. I was quite surprised when Naoko asked about you being there. Yui
was definitely shocked at this. Gendo called an assistant to play with you
while we talked.
"Why is Shinji here, Gendo?" Yui asked.
"He is here because I thought he might like to see the activation test,"
Gendo answered quietly.
"Actually, I'm canceling the test and dissolving Project E," your mother
said. "After what happened to Kyoko, I'm not taking any chances of anyone
else's mind getting trapped in these goddamn things. I don't want to leave
"I had a feeling you'd say something like that. In fact, the committee had
the same feeling, so we made a backup plan." Your father turned to a
monitor. "Agent Suzuki, if you will."
Your mother and I gasped as the monitor revealed the assistant putting his
hand on a gun he had hidden from view as he approached you. I didn't think
he'd do something like that. I didn't think anyone would do something like
that. Obviously, I was wrong.
"Now," Gendo resumed, "I'm a reasonable man, so I'll give you a choice.
You can either continue working on the project, or watch Shinji die. I'll
give you five minutes. Oh, and don't try to take him before I get back.
The man guarding your son has been instructed to shoot if you try." And
with that, he walked off to discuss something with Dr. Akagi.
Shinji, I honestly believe that those five minutes made up the longest and
most excruciating time your mother ever spent thinking. I wanted to go
after your father. I wanted to tear that bastard a new asshole, but I
couldn't leave your mother like that. I had to be there for support, or
she would have broke down right there.
Sure enough, Gendo returned exactly five minutes after he left, waiting for
Yui's answer. "All right, Gendo," your mother said, "I'll do it. But
understand this: after this, we're through. I never want to see you
"Whatever," Gendo replied, "you'll come back. After all, I've got Shinji."
After that, he signaled for the assistant to let you go. Yui immediately
ran to you.
"Mommy loves you. Mommy loves you very much," Yui repeated as she held you
close to her. She held you so tight, I could swear that only an Eva could
loose that grip. She continued to hold you for another ten minutes when
the intercom announced that she was to report to the locker rooms. As she
left, she said that she'd be back in a few hours.
That was the last time either you or I saw her again. After she changed
into the prototype for the female plugsuit, Yui went to the cage Unit 01
was waiting in. She climbed into the test plug awaiting the first
activation test of Evangelion Unit 01. I know she was afraid of the
accident with Unit 02 repeating, but I don't think anyone expected what
"Synchronization ratio at . . . 400%!?!? That can't be! It's impossible,"
screamed Naoko Akagi. "Attempting to retrieve pilot. Unit 01 isn't
acknowledging the command! It's refusing the signal!"
"No, Yui!" screamed Gendo. Why? I didn't find out until later.
"Ego border is dissolving! Attempting to reverse synchronization. Attempt
failed! The plug is ejecting, sir!" Akagi reported. She never even
thought that it could happen.
Gendo ran towards the Unit 01 as it ejected the plug and spilled the LCL
onto the catwalk, along with a plugsuit and two A10 neural interface
headsets. When he spotted the plugsuit, he did something I've never seen
him do before or ever since: he wept. I couldn't believe that a man who
was willing to order the death of his own son could weep over someone's
We tried our best to retrieve your mother, much in the same way we tried
with you. Obviously, we failed. I felt that I wasn't who should have told
you, but neither did anyone else. We told the media that Yui was lost in
an accident. Oddly enough, the press somehow got the impression that Gendo
was responsible for it.
Three days later, we held a wake for your mother. You were there, as were
Naoko, Gendo, and myself. Everyone there said very good things about her.
I doubt you remember much because you cried yourself to sleep as the first
group entered. I went home sometime around 2:00 am, after the last
The next morning, I went over to the apartment Gendo once shared with Yui.
When I got there, I was surprised to find that you weren't there. I asked
Gendo what happened, and he told me that he sent you to live with an old
friend of his. He then informed me that he got approval to proceed with
the Human Instrumentality Project.
**************END NARRATED FLASHBACK****************
Tears had long since shed from the young Eva pilot's eyes, as he listened
to Fuyutsuki's account of the past. Shinji clenched and unclenched his
right hand in fear and sheer anger towards his estranged father, Gendo
Ikari. Hearing the truth of his birth made Shinji clench his fist so
tight, that blood began to drip from his hand.
"Sir," Shinji asked in a mixture of shock and confusion, "I appreciate you
telling me what happened to my mother, but it still doesn't explain why he
left me. And another thing, why are you helping him if you wanted to kill
"I was about to tell you that when you asked," sighed Fuyutsuki. "When I
asked Gendo about what he was doing, he said that he was going to bring Yui
back from the dead. I didn't know what he meant by that. I slowly
discovered that Gendo was going to use the instrumentality project to
reunite him with her, by uniting every soul on earth.
"I realized then that he was truly mad. He deluded himself into thinking
that Yui would want him back. He thought that she loved him until your
birth. Gendo is very much willing to sacrifice you in order to resurrect
your mother. The only reason he can't right now is that you are the only
one who can pilot Unit 01. Personally, I believe that by him abandoning
you, he ran away from responsibility. However, I would shutter to think of
how you'd have turned out if he did raise you."
"He . . . ran away?" asked Shinji. [I usually run away, but so does
father. Does that mean I'll become like him? Will I become a monster like
him? Wait, I already am a monster. All I can do is hurt others. I'm no
better than him.] "Am I a monster like him?"
Fuyutsuki was a little surprised by this question. [How can he think of
himself as a monster? He isn't anything like Gendo. Wait a minute . . .
his psych evaluation!] The old professor remembered something from a
couple months ago, when he read through each pilot's monthly psych
evaluation. (Patient has an issue with misplaced guilt. Tends to blame
himself for every negative event around him. Patient's history seems to be
the root of his problems.) [Of course, I should have known. I have to do
something to help him. He doesn't deserve this hell we've put him
"Shinji," the professor said as he walked around his desk, "you're not a
monster." The old man put his hand on the young Ikari's shoulder for
emphasis. "You feel regret. If you really were a monster, you couldn't
Shinji held his tears for as long as possible, but when Fuyutsuki placed a
hand on the young man's shoulder, the dam behind his eyes finally broke.
"T-T-T-T-Thank y-y-you, sir," he managed before he succumbed to his tears.
The old professor just patted Shinji's back and let the young man finish
his weeping. The way he saw it, the poor boy had more than enough reason
to cry. He waited until Shinji stopped crying before he spoke again.
"Shinji, you said you wanted to know why I would help your father, right?"
*Sniff* "Yes, sir."
"Alright, I'll tell you. The moment I realized that Gendo was insane was
also the moment I realized that I couldn't stop him. One way or another,
he was going to follow through on his ludicrous plan. I couldn't stop him,
because the organization that funds NERV needs him to execute their plan.
SEELE is just too powerful for a single man to fight. Agent Kaji . . .
found out for himself."
"K-Kaji?" Shinji nervously asked.
"Yes, he's dead. He found out too much about the instrumentality project,
and he rescued me when SEELE abducted me after you returned from Unit 01.
SEELE sent a hit man to terminate him. That is part of why I agreed to
help Gendo. Gendo was quite useful as an insurance policy after Yui died.
If I went out and revealed the truth to the public, I would be stopped.
SEELE controls much of the UN; they control the media, as well as most
industries. It was necessary to side with your father in order to survive.
"However, I had another reason for siding with Gendo. If he succeeded, I
could be reunited with Yui as well. You've probably figured it out, but
I'll say it anyway. I loved your mother. I've never had a family of my
own, but I considered Yui to be like a daughter to me. I never told her
this, and I also feel like I failed when I didn't stop Gendo before it went
too far. So, I wanted to tell her that I was sorry. Sorry for not helping
her more. I guess I ran away as well, but that ends now."
"Huh?" Shinji was puzzled. "What do you mean sir?"
"I made a promise to myself on the day of your mother's wake. I promised
that I would tell you the truth about your mother. I would have told you
the next day, but Gendo already shipped you over to Tokyo-2. He kept me
busy for ten years, until you arrived to fight the Angels. When I saw you
fight the 4th, I thought I had plenty of time. Recent events, however,
made me realize that you and I may not have as much time as I thought. I
had to tell you now, before it gets completely out of control."
"Before what gets out of control?"
"This whole scenario, Shinji," Fuyutsuki sighed. "Haven't you noticed how
everything seems to be going to hell in a hand basket? If things continue
like this, everyone on the planet will cease to exist. I might not be able
to change things, but you might."
"Me?" Shinji asked. "Why me?"
"Because, Shinji, you pilot Unit 01. Your Evangelion is actually the key
to SEELE's scenario, as well as your father's. It keeps surprising us on
the battlefield. Now that it has its own S2 organ, Unit 01 is practically
unstoppable. It truly has unlimited power at its disposal, and yet, it
will only work for you. In essence, Shinji, you have the power to shape
our future. I know this is a bit much, but it's the truth."
Less than two seconds after Fuyutsuki finished speaking, the alarms
sounded. Time to fight another Angel. The old professor knew what would
happen next, since the commander tended to keep him up to date on the
"schedule". [It's too soon; I wanted him to be ready for this. I have to
As Shinji walked towards the door, the old man spoke, "Wait, Shinji." The
young man stopped and turned to face the Sub-commander. "I have something
to warn you of. This angel will be unlike the others in how it attacks.
Unit 01 is to be kept in stasis unless needed. If you feel that you have
to help them, do it. Do whatever you did to awaken your Eva, and save her.
I don't care anymore if your father, I mean, the Commander objects. I'm
tired of him causing pain."
"I know, sir," Shinji quietly said. "I'm tired of running. Especially
from HIM," he venomously added. And with that, Shinji left Sub-Commander
Fuyutsuki's office and headed to the locker rooms to get ready for battle.
As the Third Child left the room, Fuyutsuki leaned back in his chair and
gave a small sigh of relief and anticipation. "Now, it's all up to him. I
know you'd be proud of him, Yui. I just hope he succeeds."
TO BE CONTINUED . . .
Author's notes for 10-29-03: This is currently a work in progress.
Already have an idea of what I'm going to do with this, but I'm just
curious about what you'll think. Some of my friends already think I'm
gonna get flamed for this, but just wait until I finish this first chapter
before you start flaming me. I'd appreciate some feedback on this.
Author's notes for 11-7-03: Here it is, the first chapter of my first
attempt at a darkfic. I wondered what if Yui didn't go into Unit 01's
entry plug by choice. Then I had to wonder why. The solution was simple:
she had to protect her son. However, that would require that someone would
threaten Shinji's life. First candidate was Gendo, but I found a problem.
He would have to be an even more cold hearted bastard than the series
portrayed. I also happened to have read Random's "Acts of Kindness" and
"Innocence Lost", which gave me an idea of how much of a bastard I had to
turn Gendo into for this to work. I don't like the concept of rape at all.