- Is it in stasis at the start? I didn't see it with anyone waking up.
- How did it survive the ending, when
Ripley depressureised the shuttle cabin and sent the alien into space?
Ripley put Jones into a hyper-sleep chamber inside the shuttle before noticing that the Alien was aboard. Jones rode out the depressurization in there.
Ripley putting him into the foot of the chamber is a good indicator of where he was at the beginning of the movie, down at the foot of one of the sleep chambers where we couldn't see him. He appears at the meal table just after the group awakening when everyone is socializing and eating.