"Wake up, Shinji," ordered a voice. His father's voice.
Shinji Ikari's eyes snapped open.
"Wha-what?! WHAT THE HELL?!" Shinji, who found himself in a seated position, tried to stand up. His movement was halted by the rattle of chains. His arms, legs, and chest were all bound tightly to the metal chair in which he sat. Standing before him was his father. "Where am I? What's happening, father?"
Gendo Ikari stared back at him... and then smirked.
"Congratulations," said his father, voice mirthful.
"Father? What's going on?!"
The Commander paced around him, sniggering all the while. To Shinji, the sound of his father laughing was like having needles driven under his fingernails. "It was a fine plan, really. It had such ambition... you really are my son, aren't you? I'll admit I doubted over the years. You certainly never gave me much cause to hope otherwise, at least outwardly, but still.... good work, Shinji." He came around to the front and leaned down close to his son's face. The two Ikaris looked into one another's eyes. Shinji tried not to show fear. There was too much at stake to be afraid. And besides, he'd lived through Third Impact once already, what was that next to facing his father?
"F-Father," he consciously stuttered, trying not to lay it on too thick, "what are you talking about?"
The Commander smirked. "You're good. You're very good. You'd be better than me if you just had a few more years of practice under your belt."
"Shinji," his father said in a tone so gentle and soft that it silenced the Third Child's protests, "I know about the time travel."
Shinji kept himself from reacting.
Gendo smirked, somehow taking that as confirmation. "Shhh... shhh. It's all right. You don't have to worry anymore. I've taken care of everything."
Pure, undiluted fear shot through Shinji. "W-what? I don't know what you're talking about, father! What's going on?! Why am I tired up? Where's Misato?"
Still face-to-face, Commander Ikari said, "Son, I know you hate me. You have more than enough reasons to hate me. However, a good planner doesn't let hatred cloud his judgment of his enemies." The Commander adjusted his glasses, and, though he used his index finger to do it, Shinji understood it was meant as a one finger salute. "Or, to be blunt, you don't become Supreme Commander of NERV by being stupid."
Gendo Ikari stood up, imposing his full height over his seated, chained child. "NERV... SEELE... we engineered the Second Impact and then covered it up so completely that even the tin-foil hat loonies on street corners ranting conspiracy theories about 'the truth' work for us. We murdered three billion people and followed up with an encore of taking control of the UN and every government on Earth. We even managed to outlaw nukes. If you'd asked me twenty years ago, I'd sooner believe in Santa Claus than in that happening. And that's not even counting creating and building the Evas!
"We... I... know VERY well how to orchestrate a conspiracy. I also know when something is not going to plan. And you," he half-heartedly kicked one of the legs of Shinji's chair, "most definitely did NOT go to plan."
The Third Child rattled his chains violently and tried to rock in his chair (which was bolted to the floor). "Why am I chained up?! Father, please!"
"Tell me, when you showed up in the past, did you just decide to be a smartass? Were you so pathetic in your last life that the idea of reliving the last few months, few years, was like going to college --- a chance to reinvent yourself? To be 'cool'?" Gendo reached over to cart and picked up a two-inch thick file folder marked 'Ikari, Shinji'. He dropped it onto his son's lap with a thump. "That was your first mistake, Shinji. Wait. No. Your first mistake was standing up to me that day in the Eva Cage, the day of the Third Angel's attack. Maybe your antics and insults impressed Captain Katsuragi and the tech crews but I know I wasn't charmed. But I wasn't angry either.
"First I was confused, then... I was curious.
"I was confused because you were most definitely NOT what I'd expected. You were bold, daring, even -- if I may say so -- almost witty. I thought to myself, 'How could all these years of careful field observations and thousands of man-hours of analysis and psychological profiling be so completely and utterly wrong?'" Gendo took off his glasses and used a handkerchief to wipe off some dust. "But then you fought the Third Angel and I became curious.
"Curious as to how a boy with no previous training could pilot an Eva so well, even when it was pathetically obvious he was trying to fake clumsiness. Curious as to how a previously passive-aggressive boy, a boy who'd never stood up for himself in his life before that day, could practice such effortless violence." Gendo put his glasses back on with a fond grin. "I don't know if you know this, but I used to be quite the scrapper back in the day, and I can recognize the difference between someone who's never picked up a knife before and one who can kick my ass. And you know what? The Shinji Ikari I saw fight the Third Angel could have owned me."
Commander Ikari opened one gloved palm towards Shinji. "So on the one hand I have a boy who defies years of careful monitoring and analysis by NERV, and on the other," he offered his other gloved palm, "I have incontrovertible evidence that this boy could fight back the pounding surf itself." He weighed his palms, lowering them and raising them in turn, as if his arms were balances on a scale. "And though I wasn't sure precisely WHY you didn't make sense, I still had to adapt my plan around you. So I began to study you. Because that's what a good planner does. He (or she) can't blithely accept changes, they have to understand change. You'd be AMAZED at how the tiniest details can destroy years of labor." He chuckled. "Although in your case it really wasn't the tiny details that did it.
"I mean, really! Fighting so well in the Eva? A hundred and twenty percent synch ratio? Spouting that bullshit about individualism to Rei? Helping the Second Child overcome her childhood traumas? Then dating her?!" Gendo snorted derisively. "Good Lord, Shinji! Fourteen year-old emotional eunuchs don't become Don Juans overnight! As if your little conspiracy with Mister Kaji weren't enough of reason for me to find you out!"
Shinji closed his eyes, fighting back tears. "Oh God." He knew. He knew everything.
"Yes, I know everything, because, again, I. Am not. Stupid." He walked behind the weeping boy. "Shinji," he said, placing his hands on his son's shoulders, "you really should have let the Suzahara boy die. Or whatever it was that happened last time. Because, frankly, that miracle you pulled off with the First and Second Child was nothing less than you waving your dick in my face." He gave Shinji's shoulders a squeeze. "A good planner has to be willing to make the most extraordinary sacrifices. There's no such thing as a bloodless victory. Not outside children's manga."
"You bastard," he whispered.
"I know about the time travel. I know you've lived through the Angel War once already. I know what you told Mister Kaji. I know everything. Why, I even know the date you and the Second gave your virginities to each other -- March 24th, 2016." Shinji trembled. "And you want to know how I know all that?" He leaned down and spoke softly into Shinji's ear, "Because unlike you, I never take my eye off my enemies." He chuckled. "That and I can afford to have Section-2 run 24/7 surveillance on you."
Shinji jerked his head away from his father. "W-what... what are you going to do with me?"
"Nothing," he said. "Unlike your erstwhile allies."
Shinji gasped. "Asuka!"
"She's still alive," he replied, "on the slim chance I needed to blackmail you over the next few hours. Granted, she's in a drug-induced coma, but she'll live. That is more than I can say for Mister Kaji and Major Katsuragi, though."
"N-NO! NOOO!!" Shinji rocked violently in his chair, pulling his hands hard against their chains. The edges of the metal bindings tore into his soft skin. "YOU FUCKING BASTARD!"
Commander Ikari indulged in no such passions. "Oh, this on your head. Don't yell at me if you can't handle the high stakes of a secret, end-of-history conspiracy. I am somewhat irritated that you compromised Doctor Akagi and Lt. Ibuki. Their liquidation was unfortunate, but acceptable at this stage in my plan. I hadn't planned on destroying the MAGI, but I can't risk Ritsu leaving me a computer time bomb at this stage in the game. Still, the elevators are working, and all Rei and I need to do now is to head downstairs and start the Red Earth Ceremony."
"B-but the Seventeenth Angel hasn't--"
"--been dead for two hours," finished Gendo. "We didn't even need an Eva for him."
"Oh, between Rei's AT-Field, my own Angelic add-on," he happily waved his right hand at Shinji, "and the combined firepower of several Section-2 snipers, Mister Nagisa more than met his match."
"N-no. No! That's not possible!"
Gendo arched an eyebrow. "In a world of mecha, Angels, and time travel, is it really so hard a thing to believe?"
"Rei would never help you!"
"My Rei did."
"Y-your Rei?" He paused. "No."
Shinji Ikari roared in inarticulate rage.
"I kept one or two blank clones for myself," he explained, in a perfectly calm tone of voice, after Shinji exhausted himself, "in the event that Doctor Akagi was actually involved in your little conspiracy. Once you convinced her to destroy the Dummy Plug Production Plant it was simply a matter of flushing the tank and bringing the spares out of cold storage. As for Rei's personality transplant O/S, I just--"
"Stop," said Shinji, his voice cracking. "Please stop."
He reached for a nearby tray. Shinji's eyes widened at what his father picked up.
"It's a sedative." Gendo jabbed the hypodermic needle into the meat of Shinji's left thigh. "It'd be simpler to kill you, but somehow I imagine Yui wouldn't react well to that, would she? We can't have Unit-01 rampaging through NERV at such a delicate time. No no."
Shinji felt his strength leave him with each beat of his own heart. "You... you bastard."
"We're both bastards, Shinji," he said, removing the syringe and tossing it into a nearby steel tray with a noisy clatter. "Unfortunately for you, I'm just better at it."
The last thing Shinji Ikari heard, as he fought to keep his heavy eyelids open, was the sound of his father walking away.
"A-aaaassu...ka," he slurred.
Then there was darkness and nothing more.