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I am looking for a movie which ended when a group of young people emerge from a kind of spaceship in the far future where mankind had ceased to exist. The spaceship is a kind of intelligent spaceship (presumably with AI) which has used genetic technology to produce many babies that are also released from the space ship when it arrived in the future.

The young people emerging from the spaceship discover deformed bone, some with some kind of wings, from the past civilisation of humans. As I said this is the end of the movie.

I forgot a lot about the beginning of the movie. There was an older man, I suppose a scientist, who trained the young people in special abilities. For some reason this man died (or was left behind). One of the young people, a woman, had developed special abilities that allowed her to communicate with the space ship. Somehow the young people got trapped in the spaceship and sometimes the spaceship closed doors and sometimes it opened other doors.

I forgot how the spaceship arrived in the future. Presumably it left Earth with relativistic speed and when it returned to Earth a very long time has passed on Earth but only short time in the spaceship. But it could be also that the young people were put in stasis or that the spaceship had the possibility of time travel.

It is NOT the movie called AE: Apocalypse Earth (2013), it is also NOT the movie called Millennium (1989); as far as I remember I watched it around 1994 to 1998, but the movie could be also somewhat older.

This is an episode of the 1995-2002 run of The Outer Limits, specifically season 4 episode 23, The Origin Of Species

Fairly good description with the exception of it not being a movie, and the bones were not technically deformed; rather, they were from a genetically altered human.