If you have to pick a specific moment, the part she she was asleep naked in his bed is as good as any. However they've been together for a long time by then, that was not the first or the last time they'd hooked up.
Haha, I have some mind-screwing questions myself, but I get the impression I'd be spoiling things for others, so I'll wait. :3
Oh and yes there's actually two E7 games, both prequels. They seem to be that high quality though.
Trailer for the second game. I'd like to see a series made for this actually.
YouTube - Eureka 7: New Vision intro