Following an onboard electrical fire caused by a hitchhiking facehugger aboard the USS Sulaco, the ship ejects its emergency escape vehicle (EEV). The pod crashes into the ocean of Fiorina "Fury" 161, a bleak, storm-lashed penal foundry populated by double-Y chromosome male inmates who follow an apocalyptic Christian faith. Ellen Ripley is pulled from the wreckage, discovering to her horror that Newt drowned in her cryotube and Hicks was impaled by support struts. Suspecting something followed them, Ripley demands an autopsy on Newt, but no alien embryo is found.
Unbeknownst to anyone, a facehugger managed to implant an animal (a dog in the theatrical cut, or an ox in the assembly cut). The creature bursts forth as a swift, four-legged "Runner" xenomorph that begins picking off inmates in the ventilation ducts and oil storage chambers. Ripley reactivates Bishop's damaged data core, confirming the creature was indeed aboard the Sulaco. Soon after, Dr. Clemens is slaughtered right in front of Ripley in the infirmary, but the xenomorph unexpectedly hesitates and refuses to kill Ripley, merely sniffing her face and retreating.
Ripley scans herself in the medical pod and uncovers the dreadful truth: a Queen embryo is growing inside her chest. Realizing the Weyland-Yutani Corporation is en route under the guise of a rescue operation to weaponize the Queen, Ripley teams up with Dillon and the remaining prisoners. Lacking firearms, they lure the beast into the mold facility, trapping it in the lead works and drenching it in molten metal, followed by cold water sprinklers that cause its thermal-shocked exoskeleton to shatter. When the corporate team arrives, headed by Michael Bishop, Ripley refuses their promises of surgical removal and throws herself into the fiery furnace, destroying the alien Queen forever.