60 years has passed, since the alien vessel has cloned the two (2) occupants of the Earth vessel that was directed to investigate this phenomenon.
The clones have been re-programmed by removing certain memories and implanted with new ones.
Basically all this was interrupted with the introduction of the original wife of the male clone 60 years earlier (of course being in statis for over 60 years).
Memories emerge with some explanation... clone realises that he is married to this new found woman... love runs deep... but... the other girl is jealous as
she has always had feelings for him and hates the other woman (typical)
Anyway... the so called bad guys are humans, just like the clones (yes... planet is overrun with clones, but separated by "Radioactive" areas to ensure they do NOT encounter each other).
Jack 49 meets Jack 52... etc.
Jack 49 dies, but has impregnated the woman... Jack 52 searches for the house HE would have built for the woman and himself...
Simply: Aliens take over 2 humans, clones them and changes their memories to do their bidding, 60+ years have passed and the wife of the male emerges and helps him to remember
the things that was taken away from him, they get together, have sex and she falls pregnant to him, then they find another clone, they fight (but... 52 sees his past as well)... plan does
not go the way they want it to destroy the aliens... so clone 49 decides to die for the rest of humanity... he dies... and after x amount of years... clone 52 finally finds the place that 49 and
he would have created for the woman of their lives.