The commercial space tug Nostromo is on a return trip to Earth with a seven-member crew in stasis: Captain Dallas (Tom Skerritt), Executive Officer Kane (John Hurt), Warrant Officer Ripley (Sigourney Weaver), Navigator Lambert (Veronica Cartwright), Science Officer Ash (Ian Holm) and two Engineers, Parker (Yaphet Kotto) and Brett (Harry Dean Stanton). Detecting a transmission from the nearby planetoid LV-426, the ship's computer, Mother, awakens the crew. Company policy requires crews to investigate such transmissions, so they land on the planetoid, sustaining damage from its atmosphere and rocky landscape. Parker and Brett repair the ship while Dallas, Kane and Lambert head out to investigate. They discover the signal comes from a derelict alien spacecraft and head inside it, losing communication with Ash. Inside, they find the remains of a large alien creature. Ripley deciphers part of the transmission, determining it's not a distress signal, but a warning of some kind. In the spacecraft, Kane discovers a chamber containing hundreds of large egg-like objects. When he touches one, it opens and a creature springs out and attaches to his face through the facemask of his spacesuit. Dallas and Lambert carry the unconscious Kane back to the Nostromo. As acting senior officer, Ripley refuses to let them aboard, citing quarantine regulations, but Ash ignores Ripley and lets them in. The crew unsuccessfully attempt to remove the creature from Kane's face, discovering that its blood is an extremely corrosive acid. It later detaches on its own and is found dead. The ship is partly repaired, and the crew lifts off. Kane awakens with some memory loss but otherwise unharmed. During a final crew meal before returning to stasis, he chokes and convulses in pain, then dies as a small alien creature bursts from his chest and escapes into the ship. The crew attempts to locate it with a tracking device and capture or kill it with nets, electric prods and flamethrowers.
Brett follows the crew's cat, Jones, into an engine room and the now fully-grown alien (Bolaji Badejo) attacks him and disappears with his body into an air shaft. After heated discussion, the crew decide the creature must be in the air ducts. Dallas enters the ducts, intending to force the alien into the airlock, but it ambushes him. Lambert implores the others to abandon ship and escape in its small shuttle. Now in command, Ripley explains that the shuttle will not support four people and pushes to continue with Dallas' plan of flushing out the alien. Now with access to Mother, Ripley discovers that Ash has been secretly ordered to return the alien to the company, with the crew deemed expendable. Ripley confronts Ash and he tries to choke her to death. Parker intervenes and clubs Ash, knocking off his head and revealing him to be an android. Parker reanimates Ash's head and they learn he was assigned to the Nostromo to ensure the creature was returned for analysis at any expense, including the crew's lives. Ash taunts them about their chances against the "perfect organism." Ripley disconnects Ash and Parker burns his smashed remains with a flamethrower.
In 2179 a fire starts aboard the Colonial Marine spaceship Sulaco. The computer launches an escape pod containing Ellen Ripley, the young girl Newt, Hicks, and the damaged android Bishop; all four are in cryonic stasis. Scans of the crew's cryotubes show a queen facehugger attached to one member. The pod crash-lands on Fiorina "Fury" 161, a foundry facility and penal colony inhabited by male inmates with double-Y chromosome syndrome, a genetic mutation present in some males in the 22nd century which gives the afflicted individual a predisposition for brutal antisocial behavior such as rape and murder. The inmates, who live and work on Fiorina "Fury" 161 due to their dangerous nature and histories of violence, recover the crashed pod and its passengers. The same facehugger is seen approaching inmate Murphy's dog, Spike. Ripley is awakened by Clemens, the prison doctor, who informs her that she is the sole survivor. She is warned by the prison warden, Harold Andrews, that her presence may have disruptive effects. Ripley insists that Clemens perform an autopsy on Newt, secretly fearing that Newt may be carrying an alien embryo. Despite protests from the warden and his assistant "85" Aaron, the autopsy is conducted and no embryo is found. The bodies of Newt and Hicks are cremated. Elsewhere in the prison, a quadrupedal alien bursts from Spike. Growing to full size, the alien kills Murphy, Boggs, and Rains and returns outcast prisoner Golic to his previously psychopathic state — Golic dubs the alien "Dragon". Ripley finds the damaged Bishop in the prison's garbage dump. Just as she is leaving the area, four inmates appear and attempt to rape her, but inmate leader Dillon intervenes and beats the others with a crowbar. Ripley returns to the infirmary and re-activates Bishop, who confirms that a facehugger came with them to Fiorina in the escape pod. Ripley informs Andrews of her previous encounter with the xenomorphs[9] and suggests everyone work together to hunt down and kill it. The highly skeptical Andrews does not believe her story, and explains that even if he were hearing the truth, the facility is without weapons; their only hope is the rescue ship being sent for Ripley by the Weyland-Yutani Corporation. The Dragon ambushes Ripley and Clemens in the prison infirmary, where it kills Clemens. It initially threatens Ripley but then mysteriously spares her and retreats. Andrews orders Aaron to take her back to the infirmary, but the warden himself is dragged into the vents and killed by the monster. Ripley rallies the inmates and proposes they pour flammable toxic waste into the ventilation system and ignite it to flush out the extraterrestrial. However, its intervention causes a premature explosion and several inmates are killed. With Aaron's help, Ripley scans herself using the escape pod's medical equipment and discovers the embryo of a xenomorph queen growing inside her. She also discovers that Weyland-Yutani hopes to turn the Aliens into biological weapons. Deducing that the creature will not kill her because of the embryo she carries, Ripley begs Dillon to kill her; he agrees only if she helps the inmates kill the alien first. They form a plan to lure the Dragon into the foundry's molding facility, trap it via a series of closing doors, and drown it in molten lead. The bait-and-chase plan results in the deaths of all the remaining prisoners except Dillon and Morse. Dillon remains in the mold to distract the antagonist, allowing it to tear him apart as Morse pours the molten lead onto them. Although the beast is covered in molten metal, it escapes the mold but Ripley activates the fire sprinklers, causing its molten metal exoskeleton to cool rapidly and shatter, killing it. The Weyland–Yutani commando team arrives, including a man who looks identical to Bishop,[10] who explains that he is Bishop's creator. He tries to persuade Ripley to undergo surgery to remove the queen embryo, which he falsely claims will be destroyed, but which in reality would be used as a biological weapon. Ripley refuses and steps back onto a mobile platform, which Morse positions over the furnace. The Weyland–Yutani team shoot Morse in the leg in a late effort to stop him; Aaron strikes the Bishop look-a-like with a wrench and is shot dead. Ignoring Bishop's pleas to give them the embryo, Ripley throws herself into the furnace as the infant queen erupts from her chest. Ripley grabs it to prevent it from escaping as they both fall into the furnace. The facility is closed and Morse, the sole survivor, is led away as Ripley's recording from the first film plays for the final time in the EEV.
In 2379, two hundred years after the events of Alien 3, military scientists on the space vessel USM Auriga create a clone of Ellen Ripley, designated Ripley 8, using DNA from blood samples taken before her death. The xenomorph queen's[8] DNA has been mixed in with Ripley's, and the clone grows up with an embryo inside it. The scientists extract the embryo, raise it and collect its eggs while keeping Ripley 8 alive for further study. As a result of the xenomorphs' DNA inside her, she has enhanced strength and reflexes, blood that is somewhat acidic and a psychic link with the xenomorphs. Additionally, the xenomorph's genetic memory allows the clone to have some of Ripley's memories. A group of mercenaries, Frank Elgyn, Johner, Christie, John Vriess (who constantly whistles "I'm Popeye the Sailor Man"), Sabra Hillard and Annalee Call, arrive at Auriga on their ship Betty. They deliver several kidnapped humans in stasis. The military scientists use the humans as hosts for the Aliens, raising several adult Aliens for study. The Betty crew soon encounters Ripley 8. Annalee Call recognizes her name and tries to kill her, suspecting she may be used to create xenomorphs, but is unaware the creatures have already been cloned. The xenomorphs, having matured, escape confinement by killing off one of their own to use their acidic blood to burn through their enclosures, aware of their blood's acidity from said genetic memory. They then capture Dr. Jonathan Gediman and kill a second scientist. They damage the Auriga and kill some of those people who do not evacuate, including General Perez and Elgyn. Another crew member is cocooned for eggmorphing. Military scientist Dr. Wren reveals that the ship's default command in an emergency is to return to Earth. Realizing this will unleash the xenomorphs on Earth, Ripley 8, the mercenaries, Wren, a Marine named DiStephano and a surviving xenomorph host, Purvis, decide to head for the Betty and use it to destroy the Auriga. Along the way, Ripley 8 discovers a laboratory which contains the grotesque results of the previous seven failed attempts to clone Ellen Ripley. The surviving one begs Ripley 8 to euthanise her; she complies and then incinerates the lab and its contents. As the group makes their way through the damaged ship, they swim through a flooded kitchen. They are chased by two xenomorphs. One is killed, while the other snatches Hillard. As they escape the kitchen, the xenomorph returns and blinds Christie, who sacrifices himself to kill the xenomorph so the others can escape. After Wren betrays the group, Call is revealed to be an auton, an improved version of a human created by synthetics. Using her ability to interface with the Auriga's systems, Call sets it on a collision course with Earth, hoping to destroy the xenomorphs in the crash. She cuts off Wren's escape route and directs the xenomorphs towards him. Ripley 8 is captured by a xenomorph, while the others head for the Betty. Wren, who is already aboard, shoots Purvis, takes Call hostage and demands that she abort the collision. An injured Purvis attacks Wren and forces Wren's head to his chest just as the xenomorph embryo he is carrying bursts through his ribcage, causing it to go through Wren's head too, killing them both. The survivors shoot and kill the juvenile xenomorph. Ripley is taken to the Alien nest, where she finds Gediman, still alive and partially cocooned. The xenomorph queen, having developed a uterus as a result of her genetic contamination with Ripley 8, gives birth to a xenomorph with overtly human traits. The hybrid xenomorph recognizes Ripley 8 as its mother, killing the queen and Gediman. Ripley 8 takes advantage of the distraction to escape, and makes her way to the Betty. The "newborn" reaches the Betty and attacks Call, killing DiStephano when he tries to help her. Ripley 8 finds her way onto the ship and saves Call by distracting the hybrid. Using her acidic blood, Ripley 8 melts a hole in a window and pushes the hybrid towards it. The decompression violently sucks the creature through the hole and out into space, killing it as Ripley 8 tearfully watches on. The countdown on the Auriga continues as the survivors escape in the Betty. The Auriga collides with Earth, causing a large explosion. As they look down at Earth, Call asks what Ripley 8 wants to do next. "I'm a stranger here myself," she replies.