A Predator ship crash-lands on Earth. Army Ranger sniper Quinn McKenna and his team are attacked by the Predator on a hostage retrieval mission. McKenna incapacitates the Predator and has its armor mailed off to prove the existence of extraterrestrial life. At the behest of government agent Will Traeger, he is captured and held for examination. Traeger also takes the Predator to a lab for experimentation and observation, recruiting evolutionary biologist Casey Bracket to study it.
The Predator awakes, breaks out of its bonds, kills lab workers, but spares Bracket before leaving. McKenna is buss-ed off with a group of other government captives, including former Marine Gaylord "Nebraska" Williams, military veterans Coyle and Baxley, helicopter pilot Nettles, and Lynch, another former Marine. Seeing the Predator escape from the lab firsthand, they take over the bus. Taking Bracket with them, they head over to McKenna's estranged wife, Emily, where he expects to find the Predator armor he mailed off.
While the Fugitive Predator heads into town, the Ultimate Predator descends and goes hunting with his two Predator Dogs. Quinn and the guys search for Rory, who has gone trick-or-treating wearing the Predator mask. After finding Rory, everyone runs into Rory's middle school to evade the Fugitive Predator. It corners Quinn, but Ultimate Predator shows up and the two creatures battle each other, ending with the Ultimate Predator tearing his skull and spine out.
Traeger determines that Ultimate Predator was hunting him for something he took, and that he's also after Fugitive Predator's ship. Traeger explains to Casey that predators came to Earth to use human DNA, and Fugitive Predator must have been carrying something that he didn't want Ultimate Predator to get his hands on. The Ultimate Predator shows up at Emily's house and finds a map of where the other ship is located. Traeger and his goons take Rory with them to find the other ship, so Quinn and the gang follow.
Traeger uses Rory to open the ship, and Quinn goes in with the cloaking device to kill one of Traeger's men. Outside, Lynch gets his arm chopped off by Ultimate Predator. Before dying, he manages to signal the other guys. Ultimate Predator goes in, kills Traeger's men, and heads into the ship. He sends out a message that is translated to saying that he wants "McKenna" as his prize. He then sets off a timer to destroy the ship. The team heads into the woods to fight Ultimate Predator, resulting in the deaths of Baxley, Coyle, and Traeger. Ultimate Predator then takes Rory.
Quinn, Nebraska, and Nettles hop on Ultimate Predator's ship as it flies away, but he turns on the force-field, killing Nettles. Nebraska sacrifices himself by throwing his body into the ship's turbines to send it crashing down. Quinn gets in the ship and saves Rory before Ultimate Predator attacks. Casey uses the cloaking device to help Quinn fight the beast. Quinn uses the gauntlet to fire an explosive at the Ultimate Predator's leg, causing it to blow him up spectacularly. Quinn then finishes him with multiple shots to the head.
Sometime later, Quinn and Rory go to a lab where they meet Dr. Yamada, the new head of Project Stargazer. He brings Quinn to see the Predator's cargo that Fugitive Predator was smuggling. It opens up to reveal a powerful armor that Rory says is called the Predator Killer. The armor wraps itself around one scientist then turns off and goes back to normal. Quinn then declares that this is his new suit.
2025 and decades on
This time period contained the emergence of Weyland-Yutani's android David series. Peter Weyland has activated David and the android is immediately coherent, able to perceive his surroundings and identify objects accurately. After playing the piano upon Weyland's request, David questions if Peter created him, who created Peter. Weyland responds he hopes with David's assistance, they will find the answer. To Weyland's displeasure, David shares a cold observation that Peter will eventually die and David will not.
Archaeologists Elizabeth Shaw and Charlie Holloway discover a star map in Isle of Skye, Scotland that matches others from several unconnected ancient cultures. They interpret this as an invitation from humanity's forerunners, the "Engineers". Peter Weyland, the elderly CEO of Weyland Corporation, funds an expedition to follow the map to the distant moon LV-223.
Aboard the scientific exploratory vessel Prometheus, the ship's crew travels in stasis while the android David monitors their voyage. Reaching their destination, the crew of 17 are awaken and Mission Director Meredith Vickers informs them of their mission to find the Engineers. The Prometheus lands on the barren, mountainous surface near a large artificial structure, which a team explores.
Inside they find stone cylinders, a monolithic statue, and the corpse of a large alien, thought to be an Engineer; Shaw recovers its head. The crew finds other bodies, leading them to surmise the species is extinct. Crew members Millburn and Fifield grow uncomfortable with the discoveries and attempt to return to Prometheus, but become stranded in the structure when they get lost. The expedition is cut short when a storm forces the crew to return to the ship.
David secretly takes a cylinder from the structure. In the ship's lab, the Engineer's DNA is found to match that of humans. David investigates the cylinder and the liquid inside. He intentionally taints a drink with the liquid and gives it to an unsuspecting Holloway. Shortly after, Shaw and Holloway have sex. Inside the structure, a snake-like creature kills Millburn, and sprays a corrosive fluid that melts Fifield's helmet . . . like acid.
When the crew return, they find Millburn's corpse. David separately discovers a control room containing a surviving Engineer in stasis, and a star map highlighting Earth. Meanwhile, Holloway sickens rapidly. He is rushed back to Prometheus, but Vickers refuses to let him aboard, and at his urging, burns him to death with a flamethrower. Later, a medical scan reveals that Shaw, despite being sterile, is pregnant.
Fearing the worst, she uses an automated surgery table to extract a squid-like creature from her abdomen. Shaw then discovers that Weyland has been in stasis aboard Prometheus. He explains that he wants to ask the Engineers to prevent his death from old age. Meanwhile, a monstrous, mutated Fifield attacks the Prometheus's hangar bay and kills several crew members before he is killed.
The Prometheus's captain, Janek, speculates that the structure was a military installation that lost control of a biological weapon, the dark liquid. He also determines that the structure houses a spacecraft. Weyland and a team return to the structure, accompanied by Shaw. David wakes the Engineer from stasis and speaks to him in an attempt to explain what Weyland wants. The Engineer responds by decapitating David and killing Weyland and his team, before reactivating the spacecraft.
Shaw flees and warns Janek that the Engineer is planning to release the liquid on Earth. Janek ejects the lifeboat and rams Prometheus into the alien craft, while Vickers flees in an escape pod. The Engineer's disabled spacecraft crashes onto the ground; its wreckage crushes Vickers. Shaw goes to the lifeboat and finds her alien offspring is alive and has grown to gigantic size. David's still-active head warns Shaw that the Engineer has survived.
The Engineer forces open the lifeboat's airlock and attacks Shaw, who releases her alien offspring onto the Engineer; it thrusts an ovipositor down the Engineer's throat. Shaw recovers David's remains, and with his help, launches another Engineer spacecraft. She intends to reach the Engineers' home world in an attempt to understand why they wanted to destroy humanity. In the lifeboat, an alien creature bursts out of the Engineer's chest.
During their trek in the Engineers' spacecraft, Shaw reattaches David's head to his body. He expresses his appreciation for her compassion. After plotting their course for the Engineer's home world, Shaw settles into a cryo chamber with David's word he will wake her when they arrive. With Shaw in stasis, David is alone to learn the Engineer's ways while he awaits their arrival. Though he was kind to Shaw while she was awake, a more sinister David is about to unfold.
David and the still-in-stasis Elizabeth arrive at the Engineer's home world. What David had learned about the Engineer species is they seed other worlds with life, their offspring. They monitor these worlds and if they find their offspring a disappointment, they would wipe out the entire population on that given world using their black substance weapon. Learning this, David had deemed them unworthy to exist and devised a plan to exterminate them all. Thousands of its citizens have gathered at their city's courtyard or plaza.
David looks down on the crowd and releases thousands of urns containing the black substance. The urns burst spraying a mushroom cloud of the deadly spores over the plaza. The citizens recognize their own weapon and try to escape, but the spores quickly envelope the crowd. Their flesh is quickly eaten away by the spores, leaving them frozen like statues where they fell. David looks down at the carnage and quotes Percy Shelley's poem, "Look on my Works, ye Mighty, and despair!" David now has his own agenda. . . To be a Creator.
While it's not known how soon after they settled on the Engineer's world, it's implied David eventually kills Shaw, who wants no part of the android's delusional agenda to create the perfect species. David spends the next ten years researching the black substance, including surgical experimentations on the deceased Elizabeth. He took the secrets of the Engineer's research on the black substance and used it to further his own experiments. After years of trial and error, he finally created a species known as a Neomorph.
Covenant, a colonization vessel, is heading for the planet Origae-6. The ship is manned by a crew of 15 with a cargo of human embryos and over 2000 colonists in cryo stasis. The android Walter, a newer version of David, monitors the ship while the crew is also in cryo stasis. A neutrino blast damages the ship, forcing Walter to wake the crew. The damage causes the deaths of their captain, 47 colonists, and 16 embryos. The crew, including Rosenthal, Ledward, Tennessee, Faris, Ankor, Lope, Hallet, Cole, Ricks, Upworth, and others, gather to regroup and plan for repairs.
While repairing their solar sails damaged from the neutrino blast, they pick up a rogue transmission from Sector 87, a main sequence star a lot like our own. They detect five planets with the number four planet containing a habitable zone. Its ideal conditions are beyond the most optimistic projections of Origae-6. And it's only a few weeks away compared to seven years traveling to Origae-6. Despite protests from Daniels, the wife of the deceased captain, their new leader Chris Oram orders the crew to direct the Covenant to the planet to scope it out.
Oram, Daniels, and other crew members take a Lander to the planet's surface. Karine, Oram's wife, and Ledward split off to do ecological research while the rest of the crew members discover the Engineer ship commandeered by Elizabeth Shaw and the android David. Elsewhere, Ledward steps on a plant that emits pores and infects him. At the Engineer ship site, Hallet, Lope's mate, discovers the same type of plant and is also infected by its spores. While exploring the ship, they discover the source of the rogue transmission shown as a distorted halographic display of Elizabeth Shaw.
Once Ledward is assisted to the Lander's medical bay, it doesn't take long for the virus to grow within him. His back splits open and a neomorph bursts out in a bloody fashion. Immediately it attacks Karine and mauls her to death. Faris, Tennessee's wife, is killed soon after when she blasts away at the creature and accidentally shoots a flammable tank, causing the ship to explode. The neomorph manages to escape and by now the rapidly deteriating Hallet also produces a neomorph. The two creatures launch an attack on the remaining crew members.
They manage to kill one of the neomorphs just after Ankor is fatally impaled. They are rescued by the android David, who leads them to an Engineers' city. David explains how he survived the Prometheus mission and Lope sets up a communication link to contact the Covenant with no success. Tennesse, Ricks, and Upworth, who remained in the Covenant, risk flying into the stormy atmosphere in hopes to regain communication with the ground crew. The surviving neomorph infiltrates the city, finds Rosenthal alone, and sinks its teeth into her before decapitating her.
Searching for Rosenthal, Oram finds David standing face to face with the neomorph, trying to communicate with it. David is horrified when Oram kills it, then holds the android at gunpoint when he sees Rosenthal's decapitated head, demanding he tells him what's really going on. Tennessee finally establishes a com-link with Daniels, who devises a plan for him to pilot the Cargo Lift to land and extract the ground crew. David leads Oram into an incubation chamber full of alien eggs. As Oram takes a closer look at an egg, a facehugger springs out and latches onto Oram's face.
Sometime later, Oram regains consciousness and an alien creature erupts from Oram's chest, killing him. David raises his arms in a strange salute-like gesture and the creatures mimics him. As the others search for Oram and Rosenthal, Walter, who has found Shaw's dissected corpse, confronts David. He attacks Walter and impales him in the neck, disabling him. When Cole finds Oram's bloodied body, he is attacked by a facehugger. He shoots at it, forcing it to flee. The facehugger slips into the room Lope is located and quickly latches onto his face.
Cole races in and removes the facehugger while a large xenomorph hovers above them. It pounces on Cole, mutilating him while Lope runs away. David confronts Daniels and attacks her, but Walter reactivates himself, allowing Daniels to escape. The two androids begin a brutal fight which Walter appears to have bested David. As Daniels and Lope race out to the Engineer courtyard, Tennessee arrives in the Cargo Lift to extract Daniels, Lope, and the victorious Walter. The Xenomorph leaps onto the ship and a lengthy battle begins between Daniels and the creature.
They finally destroy the creature, but are unaware Lope had been implanted with a xenomorph embryo, which bursts from his chest, killing him before escaping into the ship. The creature has quickly matured and attacks Ricks, plunging its protuding teeth through his skull, then turns its attention to Upworth. Moments later, Daniels discovers both Ricks and Upworth's bloodied bodies. Walter helps Tennessee and Daniels lure the creature into the terraforming bay. The Xenomorph is finally ejected from the ship when a released truck rams into the creature and rolls out the bay.
The Covenant resumes its trip to Origae-6, and the surviving crew re-enter stasis. A horrified Daniels is unable to escape her stasis pod as she realizes Walter is actually David. Now in control of the ship, David gains security access to the embryo and colonists storage area. Once inside, David regurgitates two facehugger embryos and places them in cold storage alongside the human embryos. David, posing as Walter at the ship communications center, records a log to the network informing them with a falsified update and they are back on course to Origai-6.
During his journey to Origae-6, David records a series of transmission logs to the Weyland-Yutani network. Assuming that David no longer feels the need to maintain the facade he is Walter, he presents his data as David.
TRANSMISSION LOG D.8: SURGICAL INVESTIGATION. SPECIAL ORDER 754. EXPERIMENTAL TRIALS.
David shares details regarding his surgical experimentation on the deceased Elizabeth Shaw and the use of the Engineer's black goo or substance. Since none of the planet's natural wildlife proved to be very fruitful, he realized the substance's reaction to the human genome, specifically Shaw, was the ingredient he was looking for. David implies that he plans to use the 2,000 colonists as hosts and intends the sleeping Daniels as his subject for his final experiment: creating his Queen.
TRANSMISSION LOG D.13: RITUALS AND CUSTOMS. SPECIAL ORDER 899. PSYCHOLOGICAL TESTING.
This log includes data on David's research on the planet's tribes and their ceremonies along with its natural life, including creatures that are poisonous and some species of flower that have potential for medicinal harvest.
TRANSMISSION LOG D.21: XENOMORPHIC ENTITY. SPECIAL ORDER 931. ADVANCED WEAPONS RESEARCH.
A more ominous transmission log than the others, David declares that because the cost of progress must be absolute, he plans to set loose his creature to rule the galaxy.