In a prologue, business magnate Peter Weyland speaks with his newly activated android, who chooses the name David after observing a replica of Michelangelo's statue of David. The crew of the colonization ship Covenant is bound for a remote planet, Origae-6, but they discover an uncharted paradise with a threat beyond their imagination. They must attempt a harrowing escape from the planet and the dangerous alien creatures that inhabit it.

In the year 2089, archaeologists discover a star map that leads them to a distant moon where they encounter ancient humanoid aliens called Engineers. As they explore an alien structure, they uncover the truth about the origins of life and face dangerous creatures created by the black fluid leaked from cylinders. With humanity at stake, they must make sacrifices and fight for survival against the alien race. In the end, the surviving protagonist teams up with an android to travel to the Engineers' homeworld, seeking answers.