[to be fair, they just needed it for the Wunder's engine. They didn't need to stick him in it. It was more a case of studying the long term effects of piloting as a comparative against Asuka and Mari and figuring out if NERV had done anything to him over the fourteen years]

...We would have, given the chance. We were attacked almost as soon as he'd been recovered.

Bastard sent a Rei clone, so naturally he thinks its the one he's saved and we're all lying to his face.