At the beginning of the story, Earth's residents are unaware that the human species on Earth and countless other planets were established by families of transhuman and alien royalty for the purpose of later "harvesting" the resulting organisms to produce a type of youth serum for the elites on still other planets. After the death of the matriarch of the House of Abrasax, the most powerful of the alien dynasties, her children, Balem (Eddie Redmayne), Kalique (Tuppence Middleton), and Titus (Douglas Booth), quarrel over the inheritance, with Balem inheriting an enormous refinery on Jupiter and Titus declaring his intention to dismantle the youth serum trade, of which Earth is the next intended source. Protagonist Jupiter Jones (Mila Kunis) narrates that her father, Maximilian Jones (James D'Arcy), met her mother, Aleksa (Maria Doyle Kennedy), in Saint Petersburg. After Maximilian is killed in a robbery, Aleksa names their daughter Jupiter, after his favorite planet, and they move to Chicago to live with Aleksa's family.
Ellen Ripley is rescued after drifting through space in stasis for 57 years. She is debriefed by her employers at the Weyland-Yutani Corporation over the destruction of her ship, the Nostromo; they are skeptical of her claims that an Alien killed the ship's crew and forced her to destroy the ship.
In 2004, a satellite detects a mysterious heat bloom beneath Bouvetøya, an island about one thousand miles off the coast of Antarctica. Wealthy industrialist Charles Bishop Weyland (Lance Henriksen) discovers through thermal imaging that there is a pyramid buried 2000 feet beneath the ice. Weyland wants to claim it for his multinational communications company, Weyland Industries, and assembles a team of experts to go investigate. The team includes archaeologists, linguistic experts, drillers, mercenaries, and a guide named Alexa Woods (Sanaa Lathan).
In 1873, New Mexico Territory, an unnamed loner (Daniel Craig) wakes up in the desert being injured with no memory and with a strange metal object on his wrist. After killing three drifters who think he might be worth bounty money, he takes their clothes, weapons and a horse. He wanders into the small town of Absolution where the local preacher Meacham (Clancy Brown) treats his wound. After the stranger subdues Percy Dolarhyde (Paul Dano), a volatile drunk who has been terrorizing the town, Sheriff Taggart (Keith Carradine) recognizes the stranger as Jake Lonergan, a wanted outlaw, and attempts to arrest him. Jake beats up the posse sent to take him in and nearly escapes, but a mysterious woman named Ella Swenson (Olivia Wilde) knocks him out. Taggart prepares to transport both Jake and Percy to Santa Fe for trial.
Encouraged to explore as a child by her late father, Dr. Eleanor "Ellie" Arroway works for the Search for Extraterrestrial Intelligence (SETI) program at the Arecibo Observatory in Puerto Rico. She listens to radio transmissions hoping to find signals sent by extraterrestrial life. Science Advisor to the President David Drumlin pulls the funding from SETI because he believes the endeavor is futile. Arroway gains backing from secretive billionaire industrialist S. R. Hadden, who has followed her career and allows her to continue her studies at the Very Large Array (VLA) in Socorro County, New Mexico.
Two hundred years after the events of Alien 3, military scientists on the outer space vessel USM Auriga create a clone of Ellen Ripley (Sigourney Weaver) using DNA from blood samples taken before her death. They extract the embryo of an Alien queen that had been growing inside her at the time of her death, raise it, and collect its eggs for further use. The Ripley clone is kept alive for further study. As a result of her DNA being mixed with the Alien's DNA during the cloning process, she develops enhanced strength and reflexes, has acidic blood and a psychic link with the Aliens.
A fire starts aboard the Colonial Marine spaceship Sulaco. The computer launches an escape pod containing Ellen Ripley, the young girl Newt, an unidentified man, and the damaged android Bishop. All four are in cryonic stasis. The ship's scans of the crew's cryotubes show an Alien facehugger attached to one of the crew members. The pod crash-lands on Fiorina "Fury" 161, a foundry facility and penal colony inhabited by male inmates with "double-Y" chromosome patterns and histories of physical and sexual violence. After some inmates recover the pod and its passengers, an Alien facehugger approaches the prison dog.
Captain Jean-Luc Picard wakes from a nightmare in which he relived his assimilation by the cybernetic Borg six years earlier (shown in the television episode "The Best of Both Worlds"). Starfleet informs him of a new Borg attack against Earth, but orders the USS Enterprise-E to patrol the Romulan Neutral Zone so as not to introduce an "unstable element" to the fight. Learning that the fleet is losing the battle, the Enterprise crew disobeys orders and heads for Earth, where a single, damaged Borg Cube opposes a group of Starfleet vessels. The Enterprise arrives in time to save the crew of the USS Defiant which is being commanded by Lieutenant Commander Worf. After Picard hears Borg communications in his mind, he orders the fleet to concentrate its firepower on a seemingly non-vital section of the Borg ship. The Cube is destroyed after launching a smaller sphere ship towards the planet.
In 2273, a Starfleet monitoring station, Epsilon Nine, detects an alien force, hidden in a massive cloud of energy, moving through space towards Earth. The cloud destroys three of the Klingon Empire's new K't'inga-class warships and the monitoring station en route. On Earth, the starship Enterprise is undergoing a major refit; her former commanding officer, James T. Kirk, has been promoted to Admiral and works in San Francisco as Chief of Starfleet Operations. Starfleet dispatches Enterprise to investigate the cloud entity as the ship is the only one in intercept range, requiring her new systems to be tested in transit.
In the year 2058, Earth will soon be uninhabitable due to irreversible effects of pollution. The United Global Space Force prepares the first launch for the colonization of a distant planet much like our own. Meanwhile, a terrorist group, the Global Sedition, wants to interrupt the colonization to be able to take over the same planet themselves. Professor John Robinson, lead scientist of the Jupiter Mission, prepares to take his wife Maureen, daughters Judy and Penny and son Will on a 10-year mission in suspended animation to the nearby planet Alpha Prime, where they will build a companion "hypergate" to the one orbiting Earth. The project is accelerated after Global Sedition terrorists attack Earth's hypergate, but are stopped by fighter pilots, one of whom is Major Don West. When the pilot for the Jupiter Mission is murdered, West is assigned as his replacement.
In 2286, a large cylindrical probe moves through space, sending out an indecipherable signal and disabling the power of ships it passes. As it takes up orbit around Earth, its signal disables the global power grid and generates planetary storms, creating catastrophic, sun-blocking cloud cover. Starfleet Command sends out a planetary distress call and warns starships not to approach Earth.
Deux enfants, Meg et le benjamin mais non moins précoce Charles Wallace, vivent avec leur mère scientifique. Leur père, lui aussi scientifique, a mystérieusement disparu depuis 4 ans.
Following the events of Alien vs. Predator, a Predator ship is leaving Earth carrying Alien facehuggers, and the body of Scar, the Predator that defeated the Alien Queen. A chestburster erupts from Scar's body; it is a new creature that is a hybrid of both species. It quickly matures into an adult Predalien and starts killing all the Predators on the ship. A Predator's weapon fire punctures the hull and the ship crashes in the forest outside of Gunnison, Colorado.
In 1958, two U.S. Air Force pilots and aspiring astronauts, William "Hawk" Hawkins (Tommy Lee Jones) and Frank Corvin (Clint Eastwood), are testing a modified X-plane when Hawk decides to try to break a height record. The plane stalls and they are forced to eject, narrowly missing a B-50 Superfortress piloted by navigator "Tank" Sullivan (James Garner) as they parachute to safety. On the ground, Frank punches Hawk for putting their lives at risk, but their fight is broken up by engineer Jerry O'Neill (Donald Sutherland). Their supervising officer, Bob Gerson (James Cromwell), chastises Hawk for his recklessness, before taking them to a press conference, where it is announced that the Air Force will no longer be involved in space flight tests as this has now been handed off to the newly created NASA, ending the four's dreams of reaching space.
Sur Terre, dans un futur proche, l’ingénieur et astronaute de la NASA Roy McBride s'occupe de la maintenance d'une antenne de 30 km de hauteur. Celle-ci est détruite lors d’une surcharge électrique venue de Neptune, qui cause des ravages également sur Terre.