The path to paradise begins in hell.
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Jan 5, 2104.
With around 2000 colonists and 1000 embryos onboard, the crew of the colonisation ship Covenant is en route to Origae-6, a distant planet. Walter, an improved synthetic physically resembling David8, is keeping an eye on them.
The crew prepares for hypersleep on board the ship before embarking on their long one-way journey. After Captain Jacob Branson retires, the rest of the crew celebrates with drinking, gambling, and joking, as well as a final supper before their long slumber. Walter intervenes to save Upworth's life when she starts choking on her supper. The crew toasts the Covenant after Daniels gives a speech about their journey together.
Dec 5, 2104.
"Mother" notifies Walter to the impending storm that was aproaching the Covenant while Walter was attending the embryo storage chamber, still more than seven years from its destiny. A neutrino burst strikes the ship. It collides with the ship due to a nearby stellar ignition, causing significant damage and igniting multiple flames on board. Walter orders the computer to rouse his 14 human crewmates from hypersleep in reaction to the situation, however Captain Jacob Branson was cremated within his cryotube when it failed to open. Despite the loss of 47 colonists, the surviving crew was able to get the crisis under control. Oram becomes the captain of Covenant, despite the fact that he believes Daniels and the other crew members are questioning his command.
Pilot Tennessee performs a spacewalk to conduct outside repairs while the crew repairs the internal damage, and his suit's communication systems pick up a fragmented, distorted broadcast. The team is able to distinguish an unnamed human humming a classic rock tune within the image from a nearby unknown planet when the transmission is processed on board. Branson's widow, Daniels, has expressed her dissatisfaction with the detour, claiming that this new "ideal" planet is too wonderful to be true. Acting Captain Oram chooses to explore since the planet, which is only a few weeks away, appears to be even better for colonisation than Origae-6, and no one wants to go back into hypersleep after what happened to Captain Branson.
Dec 19, 2104. Day.
Tennessee, Ricks, and Upworth remained onboard the Covenant when they ultimately arrived on ‘Planet 4’ (16EG14). The rest of the group descends to the surface, where they discover a lush environment devoid of animal life. While Karine conducts an ecological survey, the others track the signal.
Two members of the security crew, Ledward and Hallett, accidentally disturb some neomorph egg sacks and become infected with the alien spore. Following the Prometheus mission, the ground crew discovers a crashed Juggernaut piloted by David8 and Elizabeth Shaw. They uncover Shaw's dog tags inside, as well as the transmission's source.
When Ledward falls ill quickly and violently, the mission is cut short. Karine assists Ledward in returning to the dropship, but Faris confines them to the med-bay. Ledward is killed as a Bloodburster emerges from his back, and Karine is mauled. Faris tries to shoot the beast, but he accidentally destroys the lander by hitting multiple gas tanks. Karine, who is on fire, is about to walk out and perish in front of her husband, Oram.
A second Bloodburster bursts from Hallett's throat nearby, killing him.
As the remaining crew members try to contact radio Covenant for assistance, the Neomorph attacks them and kills Ankor. The Neomorph is killed, but Walter loses a hand rescuing Daniels from another Neomorph. One of the Neomorphis killed by the armed security crew, while the other is scared away by a strange hooded figure employing flares. The crew follows the hooded man after being unable to contact the radio Covenant owing to ionic interference and the ship's inability to breach the planet's severe atmospheric storms.
Dec 19, 2104. Night.
They are led by the cloaked man to a wrecked alien metropolis filled of Engineer corpses. When the figuee arrives to the temple's centre, he reveals himself to be David8. To gain the crew's trust, David8 tells them that the Engineer ship accidently launched a bioweapon upon their arrival, murdering the native population. The ship crashed in the ensuing pandemonium, killing Elizabeth Shaw.
Later, David8 inquires about Walter's overprotectiveness of Daniels. Walter stated that it is his responsibility, although David8 suggests that it is out of love. He then tries to teach Walter how to play the flute so that he can compose his own music. Walter is perplexed that despite being made to be a perfect android, he is unable to create in the same way as David8 can.
However, after learning the truth about David8's research, Walter confronts him: David8 had purposefully released the the Black Goo on the Engineers and murdered Elizabeth Shaw, whose body was horrifically tortured and dissected. David8 incapacitates Walter by impaling him with a flute and seemingly killing him.
Dec 20, 2104. Night.
Rosenthal, who had been separated from the main group, is attacked and decapitated by the surviving Neomorph. When David8 sees the thing feasting on her body and tries to connect with it, Oram kills it, leaving David8 shocked.
David8 takes Oram to a laboratory at Oram's command, where he exposes his operations on the planet. After experimenting with a parasitic species that deposited eggs inside its prey and using the the Black Goo as a catalyst to genetically build a greater lifeform, he created the first Neomorphs. The larvae ate their prey from the inside out as soon as they were hatched. David8 shows Oram a chamber he has used to further experiment with and develop several eggs, and a facehugger jumps from one and implants an embryo into him. As David8 watches, a Chestburster erupts from Oram's chest, killing him.
Sergeant Lope is similarly attacked by a facehugger when the remaining security crew goes to investigate, but he is spared when Cole slices it off him, gravely scorching Lope's face in the process. Cole, on the other hand, gets murdered by a fully grown kiande amedha, while Lope's manages to leave.
In another part of the temple, Daniels faces David8, who accurately predicted that Elizabeth Shaw would not be killed in the collision. David8 confesses to killing Shaw during his emperiments before attacking Daniels.
Dec 21, 2104. Dawn.
Walter reactivates himself and saves Daniels because he is a more advanced synthetic than David8 and can self-repair. David8 is atonished Walter survived, but Walter warns him that he has undergone additional alterations to protect himself. Daniels is able to flee after the two synthetics fight. Walter is successful, and Cole is killed by the kiande amedha.
Tennessee launches a rescue in the ship's cargo transorter sled when Daniels and Lope manage to contact the Covenant. Daniels, Lope, and Walter are able to board the ship. As she attends to David8's wounds, Walter notifies Daniels that he has "expired." Walter also looks after Lope, who has sustained serious burns as a result of the acidic blood.
They are, however, attacked by a kiande amedha that was born from Oram. They use the lander's remote crane and dock to destroy the monsters.
Dec 21, 2104. Day.
The rest of the crew prepares to return to hypersleep. Upworth tends to Lopé’s wounds and Tennessee check the ships systems readying to resume on course for Origae-6. While Tennessee takes Mother offline for a diagnostic check, a chestburster emerges from Lope and killed him. It matures and kills Ricks and Upworth. Tennessee and Daniels try to flush it out into space. From the bridge, Walter keeps an eye on their progress, particularly the kiande amedha. Walter is taken aback when the kiande amedha spots him through the surveillance camera and attacks it. Walter is disappointed when the kiande amedha is flushed into space.
The crew of the Covenant returns to hypersleep as the ship returns to its original mission plan. Daniels asks Walter, while he is putting Daniels under, whether he will assist her in realising her ambition of creating a log cottage on their new homeworld. Walter doesn't seem to recall her sharing this information with him earlier. Daniels then realises she's conversing with David8, who had his own hand amputated in order to take Walter's place. Daniels is powerless to stop David8 from turning on her hypersleep pod.
David8, alone on the ship, enters the colonist-infested hypersleep bay. When David8 sees the sleeping bodies, he regurgitates two little facehugger embryos and stores them. David8 then logs a final transmission, obfuscating the crew members' deaths (save Daniels and Tennessee) by claiming that they were also killed in the solar flare catastrophe.