well, a different ship, but it'd look very identical to others, at least from the perspective of the girls. (The dorm for the girls is pretty modular.) I'd set up new threads so that people didn't have to read through all the old stuff, but new people wouldn't have to know anything that happened before and old chars could just say that they got cryogenically frozen and woke up on this new ship.
I don't honestly know what the difference is between a sequel and a reboot. I'm guessing sequel means old chars can be reused and reboot means everything starts fresh. Characters who want to be brand new again even if they were played before may be if they so choose, though if two girls used to know each other and one is brought over and one is fresh, it'd help to talk about that beforehand. Most likely, the girl who already went through this would just have known someone similar but different, and the new girl would actually be new, but it could just as easily be amnesia on the part of the new girl.
It's admittedly not a game with a lot of overarching structure. I rarely post much of anything myself and just leave the girls and monsters to get acquainted.