Ripley must face the xenomorphs again as she joins a group of Colonial Marines on their trip to the planet LV426.
The escape ship with Ripley inside is picked up by a salvage vessel. Ripley is brought to the Gateway Station space station hospital. A Med Tech checks on Ripley and then Burke walks into the room with Jones. Burke tells Ripley it has been 57 years since the escape pod left the Nostromo. All of a sudden Ripley starts to have stomach pains and as she lifts her shirt up her stomach bulges from a Xenomorph baby trying to push through shocking everyone in the room including the Doctor. Ripley cries out and wakes up from the nightmare. Later, Burke gives Ripley news on her daughter and tells her she died at the age of 66, two years ago. Ripley and Burke attend her hearing on the Nostromo incident. The committee including Van Leuwen, an ECA Rep and an Insurance Man argue with Ripley on the events and the committee finds Ripley unfit to fly. After the inquiry, Ripley tells Van Leuwen to check out LV426 and he tells her there is already a group of colonists on the planet terraforming the surface.
At the colony of Hadleys Hope, population 158, Lydecker tells Simpson the wildcatter he sent to investigate a location wants to know if he has a claim on anything he finds. Simpson tells Lydecker the wildcatter can claim anything he finds as he only sent him on company orders to that location. Newt, Newt's Mother, Newt's Father and Newt's Brother are in their vehicle when they come across the wreckage of the alien ship. Newt's Father and Mother leave to explore the ship while Newt and her brother stay behind. Newt's Mother returns and immediately gets on the radio to call for help and Newt screams when she sees her Father with a Facehugger attached to his face. Burke and Lieutenant Gorman go to Ripley's apartment and Burke tells her they have lost contact with the colony on LV426. Burke asks Ripley to join the Colonial Marines in their investigation on what happened to the colonists but she refuses. Ripley wakes up from another nightmare and then calls Burke and tells him she will go, on the condition that they are going to kill the Xenomorphs and not to bring them back.
Ripley and the rest of the crew of the Sulaco wake up from their cryosleep near LV426. While eating their first meal, Bishop performs a knife trick with and cuts himself, revealing him to be an android, which upsets Ripley. The crew has a briefing where Ripley describes the events of the Nostromo, while the crew seem to make light of the danger they are about to be in. The majority of the marines, Ripley and Burke land on LV426 and take a vehicle to explore the colony while Corporal Ferro and Private Spunkmeyer stay with the drop ship. The marines split into two squads, one led by Sergeant Apone including Private Vasquez, Private Hudson, Private Wierzbowski and Private Crowe and one led by Corporal Hicks including Private Frost, Private Drake, and Corporal Dietrich. Sergeant Apone notices the area inside the colony appears to have experienced some sort of battle. Hudson and Vasquez find a group of hamsters still alive while Hicks' squad comes across evidence of a hole from xenomorph acid, as does Sergeant Apone and his squad. The group gathers at the Operations room, which appears to have been barricaded. They find a group of Facehuggers stored in a lab including two living ones. A signal appears on Frost's motion tracker and Drake almost shoots Newt who scrambles away. Hicks tries to grab her but she bites him and Ripley chases her into a utility tunnel and into where Newt has been storing supplies. They bring Newt back to operations and Gorman asks her questions after Dietrich gives her a quick physical. After Newt ignores Gorman's attempts at questioning, Ripley tries. Newt tells Ripley her name is Newt and only her brother calls her Rebecca. Hudson locates the colonists in the Processing Station and everyone takes the ground transport to their location.
Sergeant Apone and his platoon exit the transport and move to where the large group of colonists is located. As they travel they notice the walls and floor are covered in a hard resin. Ripley realizes that if the marines use their normal weapons then they might cause a rupture in the processing plant which could cause a nuclear explosion. Gorman orders Apone to gather the munitions of his men. Vasquez gives up some of her ammunition, but keeps two, giving one to Drake. They comes across colonists cocooned into the walls including a Cocooned Woman that is still alive. The Cocooned Woman begs Dietrich to kill her and then a xenomorph erupts from her chest. Sergeant Apone uses a flame thrower to kill the xenomorph and the area erupts with alien shrieks and movement. Dietrich is grabbed by a xenomorph and she pulls the trigger on her flame thrower, bathing Frost in flames. Frost falls over a safety railing on fire and drops the bag full of ammunition, which explodes killing Crowe and wounding Wierzbowski. Wierzbowski is pulled away by a xenomorph and Vasquez starts shooting at the xenomorphs. Sergeant Apone is grabbed and pulled by a xenomorph and the remaining marines retreat back to the vehicle. Ripley grabs the controls of the vehicle and drives towards the fleeing marines. Drake is killed when Vaquez shoots a xenomorph, which sprays him in the face with its acid blood. Hudson is wounded when Hicks uses his shotgun to kill a xenomorph trying to get into the vehicle and blood splashes onto his shoulder. Ripley drives away and as she does Gorman is knocked unconscious when equipment falls onto his head. Ripley wants to leave the planet and nuke the site from orbit, but Burke disagrees as he thinks the xenomorphs need to be studied. Hicks makes the decision to leave and nuke the site from orbit and tells Ferro to come and pick them up. As Ferro is about to pick up Ripley and the others she is attacked and killed by a xenomorph and the aircraft crashes.
They salvage what they can from the crash including a set of sentry units that automatically target and shoot at targets. They try to create choke points to force the xenomorphs to come at them from only a few locations. Hicks gives Ripley a locating device to wear in case he needs to find her and then Ripley and Newt go into the lab so Newt can take a nap and Ripley gives Newt the locating device. The remaining group tries to figure out what is making the eggs and Hudson comes up with the idea that they might be like bees and have a queen that runs everything. Ripley tells Bishop to destroy the specimens when he is done with them and he tells her Burke told him to keep them to take back. Ripley confronts Burke and he tells her they are worth millions and Ripley tells him she knows he is the one that sent Newt's parents to find the alien ship. The xenomorphs try and break into the operations center, but are driven away by the sentry units. Bishop tells the group about the overload of the reactor and they decide that someone is going to have to go and use the communication dish to call the other drop ship from the Sulaco and Bishop volunteers to go. Ripley passes by a now conscious Gorman and takes a nap next to Newt. Ripley wakes up and notices the jars holding the still alive Facehuggers are empty and she and Newt are attacked by the Facehuggers. She is able to get the attention of the others by using her lighter near the sprinkler system and Hudson and Vasquez kill the Facehuggers. Ripley tells the others Burke was the one who set the Facehuggers free so they could impregnate her and Newt and get the xenomorphs through quarantine, while also sabotaging the marines' cryotubes so their would be no one who knew of his plan. Hicks is about to kill Burke when the power goes out.
The xenomorphs break into the room by coming in through the ventilation shafts in the ceiling. Hudson is dragged away and Burke is killed after he abandons the others and locks them out of the lab. Newt runs away into the utility tunnels and the others follow. Vasquez is wounded when she shoots a xenomorph and its blood splashes on her ankle. Gorman goes back to help her and they both die when he pulls the pin of a grenade when they are surrounded by xenomorphs. Newt falls into a shaft and is grabbed by the xenomorphs before Ripley and Hicks can get to her. Ripley and Hicks run to an elevator and Hicks is burned on the chest and face when he shoots a xenomorph and its blood splashes onto him. Ripley brings Hicks to the pick up site and then tells Bishop she is going to go after Newt and he is to pick her up. Ripley goes to the main xenomorph chamber and finds Newt cocooned and about to be attacked by a Facehugger. Ripley kills the Facehugger and rips Newt free. As they are leaving they come across the Xenomorph Queen and her egg chamber. Ripley sets the eggs on fire and shoots the Queen's egg sack and then her and Newt run away. The Queen rips herself off of her egg sack and gives chase. As Ripley and Newt are about to be attacked by the Queen, Bishop arrives and Ripley and Newt jump on the drop ship and it flies away. The drop ship returns to the Sulaco as the reactor explodes. As Ripley and Bishop go to get a stretcher for Hicks, Bishop is ripped in half by the Queen who hitched a ride in the landing gear of the drop ship. The Queen tries to grab Newt when Ripley gets into a power loader and attacks the Queen. Ripley opens the docking bay door and the Queen is sucked out the ship into space. Ripley hugs Newt and Newt calls her Mommy and then after putting Bishop and Hicks in the cryo tubes, Ripley and Newt get into theirs and go to sleep.