In 2379, 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 DNA has been mixed in with Ripley's, so 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, the clone has enhanced strength and reflexes, somewhat acidic blood, 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 comprising Elgyn, Johner, Christie, Vriess, Hillard and Call, arrives 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 xenomorphs for study.
The Betty crew soon encounters Ripley 8. Annalee Call recognizes her name and tries to kill her, suspecting that Ripley 8 may be used to create xenomorphs, but the creatures have already been cloned. The xenomorphs, having matured, escape confinement by killing off one of their own to use its 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 failed to evacuate, including General Perez and Elgyn. Another crew member is captured and cocooned for eggmorphing. Military scientist Dr. Wren reveals that the ship's default command in an emergency is to return to Earth. Realizing that this will unleash the xenomorphs on Earth, Ripley 8, the mercenaries, Wren, a Marine named Distephano, and 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 containing 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 don't know. I'm a stranger here myself", she replies.
