Roger Friedman‘s item is correct, according to the script: the scene where this is revealed is the last one in the movie (or at least it was in the script I read) and I thought was quite well done. In the context of the movie this subplot works okay, but if they intend to make a successful franchise out of this I’m not sure how they will navigate around the idea of a super-powered brat flying around with Daddy in sequels . It’s really the sort of thing they should’ve done to give closure to the franchise, but this will likely be the first of many new Superman films. Can you imagine if they saddled Connery’s Bond with a kid at movie # 5? The Bond films would’ve never had any legs, not that I’d really miss them. The problems with Superman Returns, however, lie less with who the child’s father is and more with the movie as a whole . It is still one big, awkward Richard Donner backslap (as I told you in a previous email) and is pretty
much Superman: The Movie with a ‘who’s the Dad’ subplot.” — C.K.