The story is set in the year 2104, 11 years after the events of Prometheus. The colony ship Covenant is on a mission to a distant planet called Origae-6, where 2,000 colonists and a crew of 15 are set to establish a new human settlement. The ship is also carrying over 1,000 human embryos to support the colonization effort. The crew is led by Captain Jacob Branson (James Franco), though after his sudden death in a ship accident, First Officer Christopher Oram (Billy Crudup) assumes command.

While en route, the ship’s systems detect a distress signal coming from a nearby, seemingly habitable planet. Oram decides to investigate, despite the reservations of the ship’s second-in-command, Daniels (Katherine Waterston), and Tennessee (Danny McBride), the ship’s pilot. They land on the mysterious planet and find an abandoned spaceship, leading them to the ruins of the Engineer civilization, tying back to the events of Prometheus.

The crew soon realizes that the planet is far from the paradise it seemed. They are attacked by Neomorphs, violent and fast-growing alien creatures. Amid the chaos, the survivors encounter David (Michael Fassbender), the android from Prometheus, who has been living on the planet after his journey with Dr. Elizabeth Shaw. David reveals that he has been experimenting with the Engineer’s biology and the black goo pathogen, leading to the creation of the first Xenomorph.

It becomes clear that David has become obsessed with creating life and has taken his experiments to horrific extremes. The crew must now fight for survival against David’s twisted creations, including the Xenomorphs, while trying to escape the planet and continue their mission.