*CUT TO THE CHASE*
NOTE: This spoiler was submitted by Jeremy
The film starts with Peter Weyland (Guy Pearce) speaking to his creation, the android David (Michael Fassbender). Weyland refers to himself as David's father and hopes to use David in seeking out the answers to humanity's creation. David questions Weyland regarding his mortality and how David will live on long after Weyland dies. Weyland responds by making David serve him tea.
In the year 2104, a colonist ship, the Covenant, is flying to its destination, an uninhabited planet called Origae-6. It is comprised of a 15 person crew with approximately 2000 colonists onboard. The android Walter (also Michael Fassbender) sets up the solar sails on the ship as he goes to check on the colony's embryos. Moments later, the Covenant is hit with a neutrino blast. Walter rushes to wake up the crew from their stasis. Captain Jacob Branson (James Franco) is trapped in his pod and is burned alive. His wife, Daniels (Katherine Waterston) watches Jacob perish as she helplessly tries to save him. The rest of the crew is taken out safely.
Daniels grieves for her husband. She watches a video of him scaling a mountain, with him telling her he wishes she were there.
Christopher Oram (Billy Crudup) assumes the position as the ship's captain. The crew gives Jacob a sendoff and ejects his body into space. The crew tends to the ship's damage. Walter then picks up a transmission appearing to be sent from another human. The rest of the crew listens to the transmission as well. Oram picks up that the transmission came from a nearby planet, which apparently has a more habitable atmosphere than Origae-6, and not to mention it would take seven years and four months before they reach Origae-6, and nobody is willing to go back into stasis. Oram chooses to go down there, despite objections from Daniels.
Before heading down to the planet, Oram expresses to his wife Karine (Carmen Ejogo) that the crew doesn't have much faith in him taking the mantle as captain.
A shuttle is deployed onto the planet while pilot Tennessee (Danny McBride) stays up on the mothership with medic Upworth (Callie Hernandez) and her husband Ricks (Jussie Smollett). The rest of the crew steps down and begins to observe their surroundings. They come across the crashed Engineer ship, which is where the transmission came from. Upon entering the ship, they see a holographic projection of Dr. Elizabeth Shaw (Noomi Rapace), who had sent the message. Daniels even comes across her dog tags.
Two crew members, Ledward (Benjamin Rigby) and Hallett (Nathaniel Dean), inadvertently step on black spores that release small clouds that fly into their ear and nose, respectively. Both men start to feel sick and weak. Karine guides Ledward back to the shuttle for medical attention as he pukes blood on her. Karine and Tennessee's wife Faris (Amy Seimetz) tend to Ledward, who starts violently convulsing. Faris quarantines Ledward with Karine still inside the room. Ledward coughs up more blood and then has something start to break out of his back. A small Neomorph emerges from Ledward's back, spilling his guts out as he dies. The creature pounces on Karine and mauls her to death. Faris returns and tries to shoot at the Neomorph, missing every shot. When Tennessee learns she is in danger, he attempts to bring the ship down to the surface to save her, but Upworth talks him out of it. She ends up hitting a tank, causing the shuttle to explode, killing herself in the process as the Neomorph escapes. Tennessee and Oram soon learn of the deaths of their wives.
Meanwhile, Hallett starts to get worse. Another Neomorph emerges, this time out of Hallett's mouth. The creature attacks a security member, Ankor (Alexander England) by ripping off his lower jaw and throat. Hallett's husband, Sgt. Lope (Demian Bichir), mourns him. The other Neomorph attacks. Walter protects Daniels from it and loses his hand to the creature's corrosive acid blood. The crew eventually shoots it dead. A cloaked man shows up and fires a flare, scaring the other Neomorph off into the darkness. It is David. He leads the crew away.
David tells the crew that he and Elizabeth came down upon the city of Engineers, but their ship released a deadly bioweapon that killed the entire Engineer population, and Elizabeth died when the ship crashed. Walter bonds with David over their shared creation and interest in the ways of their creators. David shows Walter a flute and teaches him how to play it.
Another security member, Rosenthal (Tess Haubrich), steps away to clean herself off. She then comes face-to-face with the now grown Neomorph, who rips her head off and starts devouring the rest of her. David comes across the Neomorph and approaches it gently, only for it to be shot dead by Oram moments later, to David's horror. Oram demands to know what the hell is going on and what David is up to. David explains that he used a black liquid from the planet as an experiment in creating new lifeforms. He observed that the creatures used "meat" hosts and killed them upon their birth. David brings Oram to a chamber filled with Xenomorph eggs, all of which are waiting for "Mother". He assures Oram it's safe. Oram looks into the egg as it opens up, and a facehugger pops out and wraps itself around Oram's head and neck. Soon, a creature bursts out of Oram's chest, killing him. It appears to have fully-formed limbs, and mimics David as he makes specific movements.
Walter finds David as he is looking upon the ruins of the city. David quotes "Ozymandias". Through a flashback, it is shown that David descended upon the Engineer city and unleashed the black spores upon them, killing all the Engineers. David tells Walter that humanity is a dying species, which is why they are trying to save themselves through colonization. David gently kisses Walter before ripping something out of him and disabling him. At the same time, Daniels discovers the corpse of Elizabeth, who appears to have had something burst out of her chest as well.
Lope and crew member Cole (Uli Latukefu) get found by the creatures. Lope is attacked by a facehugger and is burnt by the acid but the facehugger is killed by Cole. Cole is killed by the rapidly-growing alien that came out of Oram. Lope is taken out to safety.
David attempts to go after Daniels. He pins her to the ground and forces a kiss on her. Walter returns and starts to fight David, letting Daniels get out. Walter appears to gain the upper hand, but David is seen reaching for a knife...
Tennessee descends to the planet's surface in another lander to rescue Daniels, Lope, and Walter. The now fully-grown Xenomorph rushes to attack the crew as Tennessee flies them out of there. Daniels is attached to a harness as she swings around trying to kill the monster. Tennessee tries to fry it under the turbines, but the Xenomorph evades the fire. Daniels orders Tennessee to release the lander's crane, despite the fact that it would throw them off-balance. Tennessee does so and Daniels manages to get the creature trapped in the crane. She turns the crane on and crushes the Xenomorph.
The survivors make it back to the Covenant. Upworth tends to Lope's facial burn. Daniels and Tennessee comfort each other after all they've been through and losing their loved ones. Daniels also tends to Walter, though she senses that something may be off about him...
An unidentified life form is detected on the ship. Daniels and Tennessee run to the med-bay and find Lope dead with something having burst out of his chest. The two detect the creature's whereabouts. It stalks Upworth and Ricks as they have shower sex. The Xenomorph uses its second mouth to go through Ricks' head before killing him and Upworth.
Daniels lures the creature into the vehicle bay. Walter opens the hatch as Daniels tries to get the Xenomorph to fall out. A large vehicle starts rolling toward Daniels. She manages to duck out of the way as the vehicle impales the Xenomorph and drops out of the ship back down to the planet.
Daniels and Tennessee go back to their original mission plan as they return to hypersleep. Daniels puts Tennessee to sleep, and is prepared to have Walter do the same for her. Before she sleeps, she asks Walter if she'll help him build a cabin by the lake (referencing something she told him earlier). He doesn't immediately respond, and Daniels quickly realizes it is (unsurprisingly) David. She screams and tries to break out, but David puts her to sleep. He goes over to the refrigerator of embryos and regurgitates two alien embryos to store with the others. David then records one last transmission before heading off on his own mission.
The crew of the Covenant sets out to an uninhabited planet, Origae-6, as part of a colonization mission. A neutrino blast hits the ship, forcing the crew out of hypersleep and killing their captain.
A transmission is received by the crew, leading them to the Engineer planet that the android David and Dr. Elizabeth Shaw had set out to find. Upon arriving, two crew members are infected by spores that cause them to be hosts to two alien creatures ("Neomorphs"). The crew is found by David, who appears friendly at first but is soon revealed to harbor a dark secret.
David unleashed the spores upon the Engineers, killing their entire race to pave the way for new creations as he feels humanity must be eliminated to make way for a more advanced species. He even killed Elizabeth by using her as a host for the creatures. David fights Walter, the other droid that resembles him, and Walter at first appears to be the victor.
After most of the crew is killed by the quickly-maturing creatures, only Daniels, Lope, and Walter are left. They fight a matured Xenomorph and kill it with a crane on one of their landers. However, another monster emerges from Lope's body, killing him and two more crew members. Daniels leads that creature to its death by having a large vehicle from their bay impale it and drop it back down to the planet's surface.
The surviving crew members return to their original plan, but Daniels realizes too late that David took Walter's place and plans to continue his own mission. He has smuggled two Xenomorph embryos onboard and prepares to perform more experiments on the Covenant's colonists.