'I think it looks like a spaniel,' announced Shigeru Aoba, whilst staring intensely at the red wall. Originally it was gunmetal grey, but having been accidentally redecorated following the suicide of Dr Naoko Akagi it was now a vivid scarlet, though as the remaining Factor VIII in the blood congealed itself, it slowly shifted into a duller burgundy colour.

'Sir, do you mind?' The grunt in the biohazard suit, fighting every instinct in his body, was as polite as possible to Aoba. The recent Gehirn recruit murmured in recognition and stepped aside, noticing that the grunt looked just as threatening with a sponge as he would do with a gun. Perhaps that was why High Command (a nickname: Aoba was too sharp to think that Gendo Ikari called the shots alone, and too self-preservative to find out about SEELE) kept them all underground. After all, Gerhirn was a public organisation, and it was in its own best interests not to scare people. His curiosity satisfied, Aoba left the command centre, passing Professor Fuyutsuki on his way out. They gave each other equally cursory nods, and went about their respective businesses.

Of all the ways in which SEELE's plot could be derailed, Fuyutsuki never imagined this. Naoko committing suicide, Rei Ayanami murdered...the sort of things that bring down governments. Not that SEELE was as vulnerable as any government, but still: Gehirn was in the public eye, and heads would be likely to roll. Might he have to seek a new job? Would he have to go back to the university? It was possible that they wouldn't even take him: any scientist that didn't actually work for Gehirn or its affiliates in the Marduk institute hated them. Accepting a job from Gendo Ikari would be seen as treachery in the circles that Fuyutsuki used to keep. 'Perhaps they have a point,' thought Kyouzou. Still, it was the lesser of two evils, surely? Either work for Ikari, and keep in his machinations in check to a greater or lesser extent, or work against him, and be eliminated, or worse, ignored.

'Fuyutsuki; see me in my office. I have something to show you.' The instruction was characteristically enigmatic. What would he be shown? The door? A bullet to the face? Sometimes Gendo was really agonizingly self-important. Nevertheless, Fuyutsuki marched down to Gendo's quarters like a good little soldier, and was extremely surprised to find Gendo holding the door open for him, and smiling.
'Sit down, please.' Again, Fuytsuki obeyed. 'I'd like you to meet someone.' He gestured to the door through which Fuyutsuki had entered, as if he was a mayor unveiling a parking lot. With a movement mindful of his middle aged back, Fuyutsuki turned round, and then nearly fell off his chair. Rei Ayanami was standing in the doorway, with the same red eyes, same blue hair, same creepy smile - hell - even the same clothes.
'Gendo!' He coughed, barely able to find his voice. 'How is this possible?' Gendo chuckled infuriatingly. 'Damn it, man, tell me what's going on!'
'Certainly.'

It was revealed that Gehirn was being dissolved, but not to worry, a new organisation called NERV was to be founded to replace it. All the old staff would transfer over (with the obvious exception of Dr Akagi), and Fuyutsuki was to receive a promotion.
'You will be my new Vice Commander.' He chuckled again. 'I think you'll agree it has a pleasant ring to it.' He shifted his glasses up his face as he sat back in his chair. 'That being the case, I think you're entitled to become privy to my little secret.' He nodded towards Rei, who bowed politely.
'So she is your secret lovechild, then?' Fuyutsuki said, perturbed into comedy. 'I owe Mr Aoba some money.' Gendo stiffened in repressed anger (not that Kyouzou had ever seen Gendo feel an emotion that didn't require the justification 'repressed'), then relaxed again.
'No, Kyouzou. Rei is...our backup plan.' Fuyutsuki prepared himself for reception of another plausibly deniable truth. He knew so much now about this insane world he'd fallen into that if he ever went to the authorities (should any remain not under SEELE's thumb) they wouldn't just laugh at him, they'd intern him.

What was Rei? Rei was a clone, a receptacle for the soul of Lilith, and a potential pilot for an Evangelion. What was Lilith? Adam's counterpart, found at the centre of the Black Egg of the Geofront. What were they going to achieve with it? The Human Instrumentality Project. What was that? A new genesis for humankind. What does that mean?

It was at this point that Gendo outlined his scenario.

It was at this point that Fuyutsuki wished he had some laudanum with him.