In a formal hearing, the company questions her about the events on the Nostromo. No one believes her story. There's no evidence to back it up. Colonists have been living on LV-426 for over 20 years. The court suspends Ripley's license and sentences her to 6 months of psychometric probation.

Meanwhile, at Hadley's Hope, the colony on LV-426, Rebecca "Newt" Jordan and her family investigate some coordinates sent to them by a company representative. They discover the Derelict Ship, still intact. Newt's parents decide to take a closer look. While inside it, her father is impregnated by a Facehugger.

Back at Gateway, contact is lost with the colony. When asked to go check it out with a group of United States Colonial Marines, Ripley refuses. Burke gives her his word the only reason they're going is to wipe out these creatures. She finally agrees. She gets her license reinstated and the rank of Lieutenant.

They travel to LV-426 in cryosleep on the U.S.S. Sulaco. Once Ripley realizes an android is onboard, she's furious. "Just stay away from me, Bishop. You got that straight?" Lt. Gorman briefs the marines. Ripley tells them about her last encounter, but they don't take it seriously until she goes off on them. "Just one of those things managed to wipe out my entire crew in less than 24 hours, and if the colonists have found that ship, there's no telling how many of them have been exposed. Do you understand?"

Using a Dropship, they land on the planet's surface and deploy an Armored Personnel Carrier so the marines can search the compound. There's evidence of a battle, but no bodies. No Aliens. Ripley enters with Gorman, Burke, and Bishop. Frost picks up a signal on his Motion Tracker. It's Newt, a little girl who's survived all by herself.

Pvt. Hudson does a scan for Personal Data Transmitters. The colonists had these surgically implanted. He finds them under the main cooling towers in Sublevel 3 of the Atmosphere Processor. The marines saddle up. Inside the structure, there's some kind of secreted resin that turns the lower levels into a hive.

Back in the APC, Ripley figures out if the marines fire their weapons in there, they'll rupture the Processor's cooling system and cause a thermonuclear explosion so Lt. Gorman orders Sgt. Apone to collect ammunition from everybody. Apone puts the ammo in a bag that Pvt. Frost carries.

They resume their search and find the decaying corpses of the colonists cocooned to the walls. Cpl. Dietrich stumbles upon one that's still alive. The marines try to help, but a bloody Chestburster rips out of the colonist. Sgt. Apone fries the newborn with a Flamethrower. This wakes up the rest of the hive. Coming out of the walls, the Aliens attack the marines from all directions.

Frost's ammo bag catches fire and explodes, killing several men. Despite Gorman's orders, Vasquez and Drake kept some rounds for their Smartguns. They start blowing away Aliens. While he's trying to understand Gorman, a Warrior Alien leaps down onto Apone. "The Sarge is gone. Let's get the fuck out of here!" The marines fall back. Ripley drives the APC to pick them up.

The marines make it out of the Atmosphere Processor and decide to nuke the site from orbit. Cpl. Ferro pilots the Dropship to their location, but an Alien kills her, causing the ship to crash. The marines are stranded. They barricade themselves in the colony compound and wait for a rescue, but Bishop informs them they don't have long before the Atmosphere Processor explodes. The marines realize they need to get another Dropship from the Sulaco so Bishop goes out to pilot one down on remote.

Ripley learns that Burke sent the colonists to the Derelict Ship. "Those people are dead, Burke! Don't you have any idea what you've done here? Well, I'm going to make sure they nail you right to the wall for this! You're not going to sleaze your way out of this one! Right to the wall!" Ripley falls asleep beside Newt.

A short while later, Ripley wakes to find Burke has let Facehuggers loose in the room. She gets the marines' attention by setting off a fire alarm. Barely arriving in time, they save the two of them, killing the creatures.

Ripley tells Cpl. Hicks how Burke wants hosts for the Aliens to smuggle them past quarantine. Hicks wants to kill him. "Alright, we waste him. No offense." The power goes out. Red emergency lights switch on. The Aliens break in through the ceiling. The marines forgot to seal off the air ducts.

Hicks, Ripley, and Newt escape through some ventiliation tunnels. Hudson, Gorman, and Vasquez are killed fighting off the Aliens. Newt ends up being captured by an Alien while Hicks gets wounded by one of the creature's acidic blood. Ripley carries Hicks to the Dropship.

She has Bishop fly them into the Atmosphere Processor so she can save Newt. Locating her with a tracking device, Ripley rescues Newt from a Facehugger. When they're trying to get out, they run into the Queen Alien. It's laying Eggs. Ripley and Newt manage to get away after destroying the Queen's nest, but the enormous Alien chases them.