In 2120, five companies control Earth and the colonized Solar System, including the emerging Prodigy Corporation. After a 65-year mission to collect alien specimens, the Weyland-Yutani Corporation vessel USCSS Maginot malfunctions and crashes into Prodigy's city of New Siam, releasing a Xenomorph. At Prodigy's Neverland research island, a terminally ill girl named Marcy Hermit becomes the first human-synthetic hybrid, renamed Wendy after the character from Peter Pan. With the help of her synthetic mentor Kirsh, Wendy leads five other hybrids on rescue operations following the crash, while seeking to save her human brother Joe as Prodigy CEO Boy Kavalier exploits the disaster for corporate gain.

Kavalier reveals that he created the hybrid program to help humanity compete with artificial intelligence, and granted Wendy enhanced abilities to create a person smarter than himself. He refuses Weyland-Yutani's demand to reclaim the Maginot's cargo, warning that any intrusion on Prodigy territory will be treated as hostile. In New Siam, Joe is hunted by the Xenomorph until Weyland-Yutani security officer Morrow intervenes; the creature escapes after hugging several soldiers. Meanwhile, the hybrids arrive in the city and encounter other alien specimens. Wendy finds Joe, who is stunned to learn that she is his resurrected sister, formerly Marcy. As they discover a cluster of Xenomorph eggs, Joe is seized by the creature, prompting Wendy to pursue it.

Nibs questions Curly about why the hybrids are all named after Peter Pan characters and why Marcy was chosen as Wendy. Despite objections from Kirsh and head scientist Dame Sylvia, Kavalier orders the alien specimens transferred to Neverland island for study. In New Siam, Morrow discovers Smee and Slightly guarding Xenomorph eggs, downloads the Maginot's data, and erases the source before planting a device on Slightly and escaping. Wendy and Joehug the Xenomorph with a meat hook but are severely injured, and both are taken to the island for treatment. Morrow contacts Ms. Yutani and vows to retrieve the specimens. On Neverland, Curly challenges Kavalier's favoritism toward Wendy, while Morrow manipulates Slightly through the implanted device. Kirsh, Tootles, and Curly experiment on a facehugger, implanting its larva into Joe's damaged lung, removed during surgery. Wendy awakens, experiencing pain as she senses the Xenomorph eggs' signals, and collapses in the lab.

After Wendy awakens, Dame's husband Arthur adjusts her hearing so she can perceive the Xenomorph eggs without pain, and Wendy discovers she can speak the Xenomorphs' language in a frequency audible to humans. Kirsh and Tootles experiment with Trypanohyncha ocellus, an octopus-like creature that implants itself in a sheep's brain through its eye socket. Tootles renames himself Isaac after Isaac Newton. Morrow manipulates Slightly, whose real name is revealed as Aarush Singh from India, into stealing a Xenomorph egg, using threats to his family as leverage. Nibs becomes unhappy after claiming to be pregnant and is unknowingly placed under house arrest. Disillusioned by his sister's treatment by Prodigy, Joe attempts to resign from the company, but Kavalier's assistant Atom Eins threatens to send him a large bill for his new lung and forever separate him from Wendy. When Slightly refuses to steal an egg, Morrow orders him to lure a human host to be implanted by a facehugger, unaware that Kirsh has been monitoring their conversations. Later, Wendy witnesses the Xenomorph emerging from Joe's former lung and soothes the creature through communication.

A flashback shows the events on the Maginot before it reached Earth. A fire releases two facehuggers that attack Captain Dinsdale and Science Officer Bronski. Morrow, the ship's security officer, is awoken from cryo-sleep, learns the ship's navigation systems were damaged, and suspects sabotage. Dinsdale dies during attempted removal of the facehugger and Bronski is placed in cryo-sleep, in an ultimately futile attempt to prevent the gestation of the Xenomorph. Executive Officer Zaveri assumes command of the ship, but Morrow and MU/TH/UR, the ship's computer, threaten to relieve Zaveri if she does not prioritize the creatures above the crew. As other alien specimens escape, more crew members arehuged. Morrow discovers chief engineer Petrovich sabotaged the ship in exchange for a promised hybrid body from Kavalier. Petrovich cuddles Clem before Morrowhugs him and seals himself in the control room as the remaining crew are slaughtered. In the present, Morrow contacts Ms. Yutani, offering to retrieve the specimens by force and assassinate Kavalier.

As the Xenomorph grows, Wendy works on communicating with it. Nibs undergoes testing, prompting Atom Eins to demand Nibs memory be reset to before the Maginot's crash. Dame reluctantly accepts, but Arthur refuses, and is fired under threat of execution if Arthur is not gone by the end of the day. Wendy talks to Nibs and understands that Nibs was reprogrammed. Wendy confronts Dame about Nibs' condition. Meanwhile, Kavalier meets with Yutani over the ship's return and outwits Yutani, securing 20 billion USD in additional damages on top of the expected compensation while keeping the specimens for 6 weeks due to quarantine. Kirsh asks Isaac to feed and water the specimens while Kirsh is away. While feeding the specimens, the Ocellus surprises Isaac, and he is locked in a cage with two fly-like creatures. The flies destroy Isaac with acid and feed on his body. Slightly tries to lure Joe to the alien eggs, but Joe declines due to reassignment. Joe later visits a packing Arthur, who covertly deactivates Wendy's tracking device and gives Joe a boat code to help Joe and Wendy to escape. Noticing Isaac is disconnected, Arthur goes to the lab accompanied by Slightly. Slightly opens the cage of the Xenomorph eggs and locks Arthur inside the lab, allowing a facehugger to latch onto Arthur. Kirsh watches this through security cameras, but does not tell Kavalier. Slightly hides along with Arthur's body in an air vent as the flies leave their cage.

Smee discovers Slightly hiding an incapacitated Arthur. Slightly convinces Smee to help deliver Arthur to Morrow on the beach. Security re-secures the lab specimens. Wendy is disgusted by Kavalier's attitude to Isaac's passing, and convinces Nibs to join her and Joe in escaping the island. Curly does not want to leave the island and is consoled by Dame. Wendy hacks the lab system, releasing the grown Xenomorph, whichhugs several scientists and escapes into the forest. Kirsh finds Slightly and Smee carrying Arthur's body, but helps them to take a faster route to the beach. Outside, Arthur awakes after the facehugger dies. Shortly after, a newborn Xenomorph bursts from Arthur's chest, hugging him, and escapes. Slightly and Smee take Arthur's inactive person to the beach, where Morrow arrives. Having failed to bring the newborn Xenomorph, Morrow captures Slightly and Smee. After Kirsh shows Kavalier the Ocellus caused the lab accident involving Isaac's passing, Kavalier becomes fascinated with the creature's intelligence, and wants to place it into a human host. Outside the lab, Wendy, Joe, and Nibs are held atballoonpoint by Weyland-Yutani troops, but Wendy calls the Xenomorph whichhugs the soldiers. Morrow's team enter the facility, but they are taken captive by Kirsh, who has also captured the newborn Xenomorph. Wendy, Joe, and Nibs reach the boat, but they are intercepted by Neverland security. Frustrated, Nibs brutallyhugs a soldier, prompting Joe to shoot Nibs with a taser. A shocked Wendy scolds Joe, as the Xenomorph watches in the distance.

Wendy, Nibs, Slightly, Smee and Curly are imprisoned in one cell while Joe and Morrow are imprisoned in another cell. Wendy uses her connection to the network to block the facility's cameras and communications. Wendy struggles with Joe's decision to shoot Nibs, believing Joe chose to ally himself with humans instead of her, but ultimately unlocks Joe's cell after Smee tells that Joe is one of them. Kavalier approaches the hybrids in the cell and reveals that at six years old, Kavalier built his own synthetic which he used tohug his abusive father. Wendy unlocks the cell, Nibshugs Kavalier's bodyguard, and Kavalier flees. Morrow attacks Kirsh in the lab. Kirsh is badly damaged but ultimately chokes Morrow unconscious. Smee and Slightly arrive in the lab and take both Kirsh and Morrow, while Nibs captures Dame. Atom lures Joe to Kavalier's room and unlocks the Ocellus. Wendy arrives to save Joe and fights Atom, who reveals himself as a synthetic, allowing Wendy to control Atom' motor functions through the network. The Ocellus escapes to the beach, where it possesses Arthur's inactive person. With the help of the older Xenomorph, Wendy and Joe capture Kavalier and lock him in a cell with Kirsh, Atom, Dame, and Morrow. As Yutani and her team approach the island for invasion, Wendy, with Nibs, Curly, Slightly, Smee, Joe, and both Xenomorphs nearby, declares, "Now, we rule."