A fire breaks out aboard the Colonial Marine spaceship Sulaco, leading to the launch of an escape pod that carries Ellen Ripley (Sigourney Weaver), a young girl named Newt, the injured Corporal Hicks, and the damaged android Bishop. All four passengers are placed in Cryonic stasis. However, scans reveal a terrifying discovery: an Alien face-hugger has attached itself to one of them, indicating a looming threat. The pod crash-lands on Fiorina "Fury" 161, a hazardous foundry facility and penal colony, inhabited by male inmates with violent pasts. As the inmates recover the pod and its occupants, danger lurks nearby when a face-hugger approaches a prison dog.
Ripley wakes up to find herself being cared for by Clemens ([Charles Dance]). He informs her that she’s the sole survivor of the crash. The prison is dominated by a group of ex-inmates, led by Dillon, who have turned to a fanatical, apocalyptic interpretation of Christianity. The prison warden, Harold Andrews ([Brian Glover]), cautions Ripley that her presence might disrupt the tenuous peace within the colony. Fearing that Newt might be harboring an Alien embryo, Ripley requests Clemens to perform an autopsy. Despite pushback from Andrews and his assistant Aaron ([Ralph Brown]), the procedure goes ahead and thankfully reveals no embryo.
As Ripley's actions become increasingly erratic, she incurs the warden's mounting frustration and the inmates’ unease. A solemn funeral is held for Newt and Hicks, whose remains are cremated. Meanwhile, an unusually large Alien emerges from the prison dog, leading to chaos as it begins slaughtering the colony's inhabitants and plunges a troubled prisoner, Golic ([Paul McGann]), back into madness. In a desperate move, Ripley reactivates Bishop, who confirms that an Alien has indeed come with them in the escape pod. When Ripley warns Andrews about the imminent threat, he remains skeptical but admits they have no means to combat the creature.
After an encounter in the infirmary results in Clemens’ gruesome death, Ripley realizes that the Alien has recognized her due to the embryo she carries, opting to spare her life. Determined to eradicate the Alien, she proposes a risky plan involving the prison's toxic waste, but an explosion during the operation results in more casualties. Using the medical equipment from the escape pod, Ripley discovers with horror that she is gestating an Alien Queen embryo and learns Weyland-Yutani's sinister intent to weaponize both the embryonic and adult Aliens.
Realizing that her only hope lies in ending her own life to prevent the embryo from hatching, Ripley pleads with Dillon for help. He begrudgingly agrees under the condition that she assists the remaining inmates to confront and destroy the creature first. They devise a perilous scheme to trap the Alien in the foundry's molding area and terminate it with molten lead. Tragically, the plan leads to almost every inmate's demise except Morse ([Danny Webb]) and Dillon. In a heartbreaking act of sacrifice, Dillon draws the Alien's attention, allowing it to attack him while Morse conducts the plan.
Though the Alien is encased in molten metal, it manages to escape. Quick-thinking, Ripley activates the fire sprinklers to cool down the creature's exoskeleton, leading to its dramatic demise. As the Weyland-Yutani commando team arrives, they are led by a man resembling Bishop, who claims to be his creator ([Lance Henriksen]). He attempts to manipulate Ripley into undergoing surgery to remove the Alien Queen embryo. She stubbornly refuses and retreats onto a mobile platform held over the furnace.
In a relentless struggle for survival, the commando team tries to seize the "magnificent specimen", but with valiant resolve, Ripley makes the ultimate sacrifice by throwing herself into the furnace, ensuring that the Alien threat is eradicated once and for all. The facility is subsequently closed, leaving the lone survivor, Morse, to be led away into the unknown.
