A massive metal ring with engraved cover stones is discovered in the sands of Giza, Egypt in 1928, by an archaeologist named Langford and his young daughter, Catherine. Many years later, the elderly Catherine Langford offers Egyptologist and linguist Daniel Jackson the chance to translate the Egyptian hieroglyphs on the cover stones. Jackson accepts and travels to a US Air Force installation where he examines the stones. Special Operations Colonel Jack O'Neil arrives to take command of the project and he declares it "classified" before Jackson can begin his research.
Prior to the destruction of Krypton, the criminals General Zod (Terence Stamp), Ursa (Sarah Douglas) and Non (Jack O'Halloran) are sentenced to banishment into the Phantom Zone for insurrection and murder, amongst other crimes.
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.
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 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.
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.
Royce (Adrien Brody) awakens to find himself parachuting into an unfamiliar jungle. He meets several others who arrived in the same manner: Los Zetas drug cartel enforcer Cuchillo (Danny Trejo), Spetsnaz soldier Nikolai (Oleg Taktarov), Israel Defense Forces sniper Isabelle (Alice Braga), Revolutionary United Front officer Mombasa (Mahershala Ali), death row inmate Stans (Walton Goggins), Yakuza Inagawa-kai enforcer Hanzo (Louis Ozawa Changchien), and a general practice doctor Edwin (Topher Grace). An unnamed soldier dies when falling to the ground due to parachute failure.
In the future, humanity is preparing to launch an attack on the homeworld of an alien race called the Formics who had attacked Earth and killed millions. Over the course of fifty years, gifted children are trained by the International Fleet to become commanders of a new fleet for this counter-attack.
In the 23rd century, Earth has become a space-faring federation. While colonizing new planets, humans have encountered an insectoid species known as Arachnids or "Bugs", with their home being the distant world Klendathu. The bugs appear to be little more than killing machines, though there are suggestions that they were provoked by the intrusion of humans into their habitats.
In the year 2293, retired Captain James T. Kirk, Montgomery Scott, and Pavel Chekov attend the maiden voyage of the Federation starship USS Enterprise-B, under the command of the unseasoned Capt. John Harriman. During the voyage, Enterprise is pressed into a rescue mission to save two El-Aurian ships from a strange energy ribbon. Enterprise is able to save some of the refugees before their ships are destroyed, but the starship becomes trapped in the ribbon. Kirk goes to deflector control to alter the deflector dish, allowing Enterprise to escape, but the trailing end of the ribbon rakes across Enterprise 's hull, exposing the section Kirk is in to space; he is presumed dead.