This is rated not for sex scenes per se but discussion of sex and potentially disturbing themes. It's also Shinji/Kaworu, but not in a WAFFy way at all.
When you think about it, the only difference between Gendo and a psycho crazy stalker is that Yui loved him back.
The love of an Ikari is a dangerous, powerful, and utterly fucking insane force, as Shinji also demonstrates in the second Rebuild movie. 'Screw the world, I want Rei.'
Shinji stared down at Kaworu, who had perched in the palm of his hand. "Let me see if I've got this straight. If I don't kill you and you merge with Lilith, our souls will become one. I'd be mingled together with you… And the rest of humanity," but Kaworu was the important one, "And we'd be together forever."
"But you would have lost your individual existence," Kaworu pleaded with him.
Shinji considered exactly how much existence as an individual had ever done for him.
"If you don't do this, the world you have protected will be destroyed." Sad but trusting red eyes met his, even though the Eva's armor was between them.
Shinji thought about the world he'd fought for. About the ruined city of Tokyo-3, about the tank of Rei clones, about his father's abandonment.
"The home you have won't be there to return to." Kaworu, dear innocent Kaworu, thought that having a home meant having people who cared about Shinji, would certainly lead him to happiness.
Shinji thought of Misato, of dead Kaji, of broken Asuka whose mind he couldn't fix. Of how he hadn't been able to protect Rei.
It didn't take Shinji very long to make his choice.
To turn his hand into a fist, grab the silver-haired angel (who looked so much like Rei, he couldn't kill someone who looked so much like Rei), and try to thrust him into Lilith before he had time to react.
Damn, Shinji thought as his arm fell off, cut by Kaworu's AT field, the light of his soul. Well, of course such a pure soul would have a bright light. This wasn't going to be easy.
"Shinji?" Kaworu asked now, hovering a few meters away, wondering why, but even if he sounded startled and maybe a little hurt by Shinji not accepting the gift of his death, worried by what he interpreted as Shinji's lack of desire to live that was better than being calmly resigned to death.
Shinji grabbed his arm and held it to the stump, sync ratio climbing and giving him access to the memories of his mother, the one who knew more about the EVA's capabilities than anyone else.
As she watched the scene before her, Rei's attention wavered.
"We've regained contact with Terminal Dogma!" Maya announced as an image of Lilith's chamber appeared in front of them.
The voice of the Fifth Child, the Seventeenth Angel, sounded… worried? "-ji, please, you must-"
"Get back here and be one with me!" Shinji roared, the berserk now-winged Eva pursuing Kaworu up and down the chamber both horizontally and vertically as the angel fled from him.
"But the Lilim…"
"Fuck the Lilim! Fuck the world, it's fucked me enough times! I've spent my life alone in a sea of assholes, and if you think I'm letting you get away you've got another think coming!" Shinji said, swiping at the air with grasping claws, only his smaller size letting the angel keep slipping out of them, a little grey mouse barely escaping a ravenous cat, only there was nothing playful about Shinji's pursuit. "You're the first person in my entire life who's ever been nice to me! Like hell I'm letting you get away!"
Everyone stared. Most of them because they were having trouble processing what the hell was going on, but Gendo because this was when he realized that Shinji wasn't just a lump of flesh that took Yui's attention away from him, he was Gendo's son.
Gendo had worked for instrumentality all this time in order to get Yui back. Gendo had been abandoned by his own mother. Despised by his classmates and never given a chance by his teachers, while Shinji had retreated Gendo had lashed out at the world.
Until he met Yui. Yui, who accepted him. Yui, who showed him love and kindness.
And because of this, Yui was the one he would do anything for. Make loli clones of her. Sleep with Akagis who were utterly repulsive by comparison to his goddess. Stalk and kill anyone else who even thought about putting a move on her. Yui was just lucky she'd loved him too, because the one thing Gendo wouldn't have done for her was give up on obtaining precious, precious Yui for himself.
Well, this wasn't how Gendo had intended to bring about instrumentality, but eh, close enough. Power off the scales or not, the Seventeenth Angel wasn't going to hold out much longer, not with his son (obviously the superior model, with the addition of Yui's genes) after that pretty little head.
Time to start figuring out how to apologize to Yui for how he'd treated her baby. 'Well, in my defense, you knew I was a heartless psycho potential stalker when you married me, everyone warned you,' might not cut it, even if he could point to Shinji as proof it was in the genes and really, Gendo just couldn't help it.
It was entirely Yui's fault for being so, so Yui.
"This is your fault for saying you loved me! No one's ever said that to me before!"
Gendo nodded. The angel had clearly been asking for it.
"Death is freedom? Bullshit! Stop trying to run away! No matter where you run, I'll find you and make you mine!" Shinji declared. "If you kill yourself, I'll kill myself and come after you, so there's no point in stopping Third Impact anyway!" Kaworu couldn't save Shinji's life by dying. "Hold still and let me have you forever!"
Yes: if it weren't for the fact she was still alive in there, Gendo would have followed his love and his life into death. And if Yui'd tried to run? Gendo's fondness for bondage had come from wanting to make sure that she would never leave him. Never ever. Angels could be restrained, so this Kaworu was just lucky Gendo had already disposed of the Lance.
One of his minions reported, "We've detected another AT field! It's exiting Terminal Dogma, exiting the atmosphere at incredible speed! Headed for… the moon?"
"Rei?" Fuyutsuki murmured, surprised.
Gendo folded his hands. What did she intend to do?
A few more seconds ticked by before Shinji whooped to see the weapon lowered into the hands of his Eva. Questions like 'why are you floating and glowing?' were completely unimportant compared to the fact that Shinji now had a weapon that could keep even Adam and Lilith pinned down, a weapon that would definitely let him capture Kaworu. "Thanks, Rei! Help me corner him!" Shinji grasped the long spear and started heading towards his prey. "I'm going to do what I should have done earlier!" When Kaworu was as good as offering himself to Shinji, offering him touch and love and Shinji damned himself for a fool for not taking advantage of that offer.
If Gendo hadn't been Gendo, he might have felt a little sorry for the angel. Instead, Misato was unable to get his attention when she asked for orders or explanations or whatever because he was off in a happy place involving Yui and mighty spears.
Since Instrumentality would allow all of them to create paradises, Gendo was looking forward to his second honeymoon. Yui might want to see her son get married before the two of them took off to float around the universe together for all eternity, but it would take some work to make his son stop banging the angel long enough for her to have her wish.