Neon Genesis Evangelion: Second Coming

Dark pasts

Shinji walked into his father's office. He hadn't been here in a while, not since unit 03 had been contaminated by the 13th angel, or was it the 15th. They all ran together now. This place always gave him the creeps. He walked up to Gendo Ikari's desk. The chair turned and revealed his father, light glinting off his glasses.
"You said you found something." Shinji said.  "In her psych profile."
"I did.  But you won't like it." Gendo said as he slid the folder to his son.   Shinji opened it.  He couldn't believe it.  Her mother had committed suicide in front of her.  He kept reading.  She pushed her own daughter aside for a doll, she had been abused by her foster parents.  He went to turn the last page before his father grabbed his hand.  "Stop there." Gendo said.
"What, why, what's in here." Shinji said.
"It's not the time." Gendo said.  "It can't be confirmed or not, it's better you don't know it."
"Alright." Shinji said closing the folder.  "Thanks."
"Keep her safe son." Gendo said. 
"I will." Shinji said and left the office.  Gendo waited until the door closed before he contacted fuyutsuki. 
"Are you sure." Ikari asked
"Yes commander, your report on Asuka is accurate." Ikari cut the connection.

Shinji walked down NERV's hallway.  His life just kept getting more confusing.  First he finds out his father used to cut, now asuka.  He thought back to that day in the hospital.

Flashback
"And the most damning part of it is, you beat the fucking game, you beat fate.  You did it and lost nothing." Shinji said.
"Your wrong." Gendo said.  "I lost everything." 
"What." Shinji said
"Later, you have enough to worry about." Gendo said turning around. "keep an eye on asuka, she will need you."
Shinji stood their as the door closed. Then he went to the door. The hatch slid open. "What did you lose." Shinji asked. Gendo stopped in his tracks.
"Shinji, I know haven't been much of a father to you." Gendo said.
"Answer the question" shinji said.
"I lost your mother, and my son, and the worst part is, they were both my fault." Gendo said.
"What." Shinji said.
"When your mother told me that we were expecting, I was ecstatic, I could hardly wait to be a father, and I had hoped to be the best father I could be to you." Gendo said. "But then, I started thinking about what I did for a living. The idea of raising a child in the world, knowing what I knew, was to much to bare. I became distant and unenthusiastic."
"I find all of this hard to believe." Shinji said. "Considering everything that's happened."
"I panicked, I had to keep you as far from me as possible to keep you safe, then when we discovered the third child for Eva unit 1, I thought I had done it, then it turned out to be you, I'm sure i should have seen it coming." Gendo said
"That still doesn't explain how you treated me." Shinji said.
"No it doesn't. Shinji when I left you on that curb, it was the hardest thing I've ever had to do in my life." Gendo said. "I didn't think I could live with myself." He walked over to Shinji and rolled up his sleeve. There were small white scars all across his arm. "I went down a dark path. I wouldn't be here now if it wasn't for ritsuko, she helped fill the void left by your mother." Gendo continued. "Ever since I left all I wanted to do was protect you, which meant keeping you away. I knew we needed you, but a part of me wanted you to leave, run away, keep as far away from me and Eva as possible, so I tried to make you leave, if I acted the way I did, I thought you would try to get away from me but you didn't, and I'm grateful." Shinji let it sink in, tried to absorb what his father had told him.
"Well, you weren't there three years ago, but you are now." Shinji said. "Maybe we can try again."