Two centuries after Ellen Ripley's death, doctors aboard the space station Auriga clone her using a blood sample taken from Fiorna 161, in hopes of harvesting the queen embryo that was incubating inside of her when she was trapped on the remote penal planet. Finally succeeding after numerous attempts, they remove the alien and repair the clone for further study. Before long, the Ripley clone has gained consciousness, and displays superhuman capabilities that suggest it possesses alien DNA. When Ripley discovers that General Perez (Dan Hedaya) is keeping the queen in a heavily fortified room of the space station, she warns the military man and his scientists that the creature cannot be contained no matter how hard they try. Meanwhile, General Perez has hired a crew of space pirates to deliver the cryogenically frozen bodies of another ship to the Auriga so they can be used to breed more aliens. The leader of the pirates is Johner (Ron Perlman), a gruff mercenary who engages Ripley to no avail. When Call (Winona Ryder), one of Johner's crewmembers, admits that she was sent to assassinate Ripley, General Perez attempts to have the pirates executed. The result is a tense standoff between the pirates and the military men, with the aliens causing havoc after breaking free of their containment cells. Attempting a daring escape, Ripley and the pirates discover the lab where she was cloned before being forced to swim through the mess hall, which has been submerged in water during the aliens' escape. Discovering a carefully guarded secret about Call's past, Ripley attempts to convince her to alter the Auruga's course, which was set to Earth when the ship went into emergency mode. With the fate of mankind hanging in the balance, Ripley is captured by the aliens and taken to their nest, where she comes face to face with the mutated results of the scientists' experiments.