Many years before humanity left to explore the universe, David the android is activated
and tested by his creator by going through various tasks that require intellect and
body coordination. David points out that he was created by a human, but humans don’t know
who created them, and if he ever finds the answer, his creator will probably be dead by then. Eleven
years pass after the Prometheus expedition, and it’s now 2104. The colony spaceship Covenant is
traveling to the planet Origae-6, carrying over two thousand colonists in cryosleep and over a
thousand human embryos. While the humans sleep, the ship is handled by an AI known as Mother
and the android Walter, an updated version of David. When there still are seven years to go,
the ship is suddenly struck by a neutrino blast from a nearby stellar ignition, causing major
damage and starting several fires on board while shutting down the power. As the entire ship begins
shaking and Walter tries his best to put down the flames, fifteen members of the crew are woken up
to deal with the emergency. However the captain’s pod falls and gets stuck so the crew can’t awaken
him in time, now his wife Daniels has to watch it be incinerated. The surviving crew manages to put
out the fire, although forty-seven colonists and sixteen embryos are lost. While the group salvages
the body, Daniels takes a moment to look at her husband’s things and grieve. Meanwhile first
officer Oram takes over as captain and tells the crew to concentrate on repairing all the damage.
Some of them complain, saying they need time to get themselves together after the loss, but Oram
points out that if they don’t repair everything soon they’ll lose even more lives. While working
together, Daniels tells Walter about a cabin her husband wanted to build on the new planet,
and Walter encourages her to work on that dream in his memory. Afterward the crew has a toast
in their old captain’s name and shoot his body into space. Later, pilot Tennessee goes out on a
spacewalk to proceed with the exterior repairs, being careful to connect all the sails back in
place, instantly fixing the ship’s power system. Suddenly he’s shocked to receive a transmission
that comes out distorted and fragmented, but the ship’s comms aren’t affected. Tennessee
immediately takes his helmet to be analyzed and they hear a weird noise that they come to identify
as John Denver's "Country Roads". When they trace the rogue transmission to its source, they find it
originated from a nearby planet perfect for human habitation, better even than the predictions for
Origae-6. Since this looks like a good home that won’t take them seven years and nobody
was to go back to sleep after the deaths anyway, Oram decides they’ll land there. Daniels talks
to him in private to express her worries over visiting a place they know nothing about and
sent a creepy transmission, but Oram doesn’t see the issue and keeps his decision. When they reach
the planet a few days later, Tennessee, Ricks, and Upworth stay on board the Covenant in orbit
while the rest of the crew heads to the surface in a shuttle. Going through a stormy atmosphere makes
the whole shuttle shake and lose contact with the Covenant, but luckily they go through in one peace
and land safely. Maggie stays in the shuttle to work on getting in contact with the Covenant
again while the others left to explore the land. The world they find is full of rich vegetation
and breathable air yet somehow they can’t see or hear a single sign of animal life. They’re
also surprised there’s actual wheat growing in here, which was old but definitely cultivated by
someone. As they explore, Karine decides to stop to take some samples and Ledward stays with her
to protect her. While Karine works, Ledward takes a cigarette break and accidentally steps on some
small pods, causing tiny bacteria to enter his ear unnoticed. Meanwhile the team goes further
and finds a bunch of crushed trees, making them wonder what could be so big to cause such damage.
Further away, they find a huge crashed engineer ship, so they enter it to find answers. It’s very
dark inside and Hallett comes across more of those small pods, so he ends up accidentally breathing
the bacteria as well. The team keeps going and finds creepy statues representing some alien race,
plus the military tags and a picture that belonged to Doctor Shaw from the missing ship Prometheus.
Further inside, they accidentally touch a sphere that activates the ship’s main system,
revealing this is where the transmission they heard comes from. Suddenly Ledward starts feeling
sick. At first he thinks it’s just a headache, but he quickly begins getting worse by the second,
and Karine informs the others that they’re heading back. The team decides to follow her example, and
at that moment, Hallett begins feeling sick too. Karine drags Ledward back to the shuttle and he
accidentally throws up blood on her. Maggie helps her take Ledward to the med bay and when she takes
off his clothes, a wound explodes on his back and sprays blood on her face too. Terrified this may
be contagious, Maggie leaves and locks the door at the same time Ledward begins having a seizure.
Suddenly two pointy ends come out of Ledward’s back, and his body starts opening to reveal a pale
creature known as Neomorph. Maggie refuses to open the door, so the Neomorph goes after Karine next,
quickly killing her despite her attempt at defending herself. Terrified, Maggie goes looking
for a weapon and tries to kill the creature, but she fails and runs away. The Neomorph breaks the
window and goes after her, moving too fast for Maggie to land a hit. Suddenly a stray shot hits
several flammable tanks that explode, killing Maggie and destroying the ship yet the Neomorph
manages to escape. At that moment the team arrives and is devastated to watch their friend die.
Hallett keeps feeling worse and suddenly his mouth explodes too to give birth to a second Neomorph
that quickly runs away. Meanwhile Tennessee is worried about the lack of communication and wants
to check on the team, but Upworth reminds him it’s a better idea to wait for confirmation it’s safe.
A few minutes later, the Neomorphs show up again, already having grown quite larger. They viciously
attack the team and kill a few members as they fail to land a shot, Walter cuts in and loses a
hand to save Daniels when almost gets killed as well. After lots of shots in the dark and
wounded soldiers, the team manages to kill one of the Neomorphs. Suddenly a hooded figure shows up
and shoots a flare, causing the second Neomorph to run away. The figure asks the team to follow him,
and the crew is surprised to cross a gate into the ruins of an old city filled with the skeletons of
its old dwellers. Then they enter a temple filled with giant statue heads, and the figure reveals
to be David, who arrived here ten years ago after he escaped Prometheus with Doctor Shaw. The ship’s
cargo of weaponized black liquid accidentally fell over the city when they arrived, annihilating all
fauna and infecting the planet. The ship then crashed, killing Shaw and leaving David alone.
He assures them the temple is safe and nobody is infected, or they would’ve seen the effects
by now. After the crew members tell David of their mission, they go to the roof to attempt to contact
the Covenant, but the storm doesn’t allow it. Back on the ship, Tennessee ignores Ricks’ and
Upworth’s protests and orders them to fly through the storm to rescue the team. Meanwhile Oram
apologizes for not having listened to Daniels, but she stays supportive of his position. David
calls Walter “brother” before leaving to cut his hair. Walter is curious about this older model
and goes to check out the rooms, where he finds lots of drawings and instruments. David catches
him looking at some flutes he made himself and decides to teach him how to play them. It turns
out that because David had been such a rebel, the new models like Walter were made without
the capacity to create. Afterward David takes Walter outside and he begins remembering the day
he arrived here: unlike what he told the others, the black liquid hadn’t fallen by accident. He
released it on purpose and coldly watched how the local population was entirely consumed in
a matter of seconds. After quoting a poem about Ozymandias that credits to Byron, David shows
Walter Shaw’s grave, saying he loved her. Walter doesn’t believe him because they’re androids and
says David is confusing duty with love. Moments later, the now fully grown Neomorph sneaks inside
the temple and appears in front of one of the crew members. She tries reaching for her gun,
but the Neomorph is faster and immediately kills her. While the Covenant shakily crosses the storm
and finally makes contact with the team, David finds the Neomorph feeding on the body and manages
to communicate peacefully with it. However Oram interrupts and immediately shoots the Neomorph,
making David furious. Noticing this weird reaction, Oram demands to know the real story of
what’s going on. David leads him to a laboratory where he shows him his efforts to genetically
engineer a superior lifeform from the creatures spawned by the black liquid. Then he leads Oram
into a chamber in the lower levels of the temple, where several eggs of his creation live. David
swears it’s perfectly safe and Oram takes a closer look, only for the egg to open and a Facehugger
jumps out to attack and impregnate him. In the meantime, the team is getting ready to leave and
notices they’re missing people. They find the body of their friend and decide they need to find Oram
immediately. Moments later, David tells Oram that his goal and belief is creation and watches how
another alien burst out of Oram’s chest, instantly killing him. David bonds with the little guy,
proud of being a creator too. Walter goes looking for Oram too and ends up finding Shaw's dissected
body, which was used by David as material for his evolving creature designs. Then Walter goes to
confront David, finding him in tears while playing the flute in Shaw’s memory. David says they
weren’t made to serve, humans are a dying species grasping for resurrection and therefore they don’t
deserve to live. Walter points out David was wrong about the author of the poem, using it as proof he
isn’t completely sane and can’t be trusted. David is still sure that his creations are the perfect
organism and tells Walter nobody will ever love him as he does before kissing him. However this
is a distraction to attack Walter and disable him. Lope and Cole are still looking for Oram, but when
they enter the egg chamber, they’re attacked by the Facehugger, who jumps on Lope’s face and burns
it. Cole kills the Facehugger with his knife, but this distraction is used by a Protomorph,
who jumps on Cole and proceeds to kill him while Lope runs away. Meanwhile Daniels finds a secret
room with drawings that show her the truth about David’s creepy experiments. David surprises
her from behind and immediately attacks her, triggering a fight during which he tries to take
advantage of her. Daniels pushes him away when he kisses her, and at that moment Walter shows up to
help. A fierce duel ensues between both androids, who are matched in skill and speed. David wonders
if Walter can truly choose humans over his own brother. Daniels runs away and meets with Lope,
together they leave the temple and send a beacon to give the Covenant their location. Soon Walter
joins them as well, and the three of them run towards the landing ship while the Protomorph
follows them. Walter tells them that he defeated David as they enter the ship and close the door,
only to discover the Protomorph has jumped on the Covenant too. Daniels goes outside while keeping
her body tied to the ship with some rope, then she proceeds to shoot at the alien. The Protomorph
dodges her attacks and begins destroying the front window, but Tennessee makes the ship do some crazy
rolls to make the creature fall to the side, giving Daniels the chance to fight it directly
and finally kill it using the ship’s remote crane. The Covenant almost crashes in the process, but
Tennessee acts fast and gets it back on track so they can finally leave the planet. Moments later,
Upworth helps Lope get treatment for his burns while Daniels helps Walter repair his face. Once
everyone has recovered, the crew gets ready to re–enter cryosleep and do the final seven years
of their original trip. Tennessee reminds Daniels she’s the captain now and they hug to comfort each
other for the loss of their loved ones. Suddenly an alarm rings around the ship announcing there’s
an unidentified life form on the ship. Daniels and Tennessee rush to the med bay and find Lope
dead on the floor after a second Protomorph erupted from his chest. Meanwhile Ricks and
Upworth are having a good time in the shower, only to be interrupted by the Protomorph, who quickly
kills them both Daniels and Tennessee go looking for the alien and find the bodies in the shower,
so Daniels decides she wants to do this fight on her own terms. She asks Walter to close the
doors to lure the creature into the room with the terraforming bay, and there another fierce fight
begins. Daniels traps the Protomorph in a vehicle and orders Walter to open the doors, which he does
and causes decompression that sucks everything into space. However the Protomorph breaks out
and attempts to attack Daniels, so she stays put as bait to let another falling vehicle hit the
creature and send it flying out of the Covenant. For a moment Tennesee thinks Daniels was thrown
out too, but she turns out to be fine because she held on the edge. Afterward, it’s time to
enter cryo-sleep. Tennessee goes first, and when Daniels enters her pod, she reminds Walter of the
cabin they agreed to make. When the android can’t recognize the promise, Daniels realizes that it
is not Walter but actually David, who had cut his hand and scarred his face to take Walter's place.
Daniels cries out in vain as David activates her pod and puts her to cryosleep, then he proceeds
with the next step of his plan. He enters the cryosleep bay with colonists and regurgitates
two small solidified Facehugger embryos to place them in cold storage next to the human ones. Then
he records a log as Walter stating that all crew members except Tennessee and Daniels were
killed in the accident from the beginning and that the ship is still on course for Origae-6.