The film centers on Teddy Gatz, Jesse Plemons, a man tethered to conspiracy theories who drags his mentally handicapped cousin Don Aidan Delbis into a shadowy mission to “fix” society. They head to a store to stock up on supplies, and although Don quietly doubts the plan, Teddy treats it as a mission of great importance that must be carried out.
Michelle Fuller, Emma Stone, is a high-profile CEO at Auxolith. After a long day, she drives home to a terrifying scene: Teddy and Don, wearing paper Jennifer Aniston masks, spring from the bushes to abduct her. She fights back and nearly escapes, but Teddy ultimately subdues her with a needle and she loses consciousness.
Back at their house, the two men shave Michelle’s head and cover her body with a histamine cream. When she wakes, Teddy explains that he and Don believe she is an Andromedan alien sent to exterminate humanity. The acts of shaving and the cream are meant to suppress any powers she might possess, and Michelle recognizes that her absence will trigger a police search. She pretends to confess to being an alien, but Teddy reveals there are three days until the lunar eclipse, at which point they plan to present her to the mothership. Meanwhile, Don grapples with growing unease as he watches Michelle on their basement camera.
A flashback reveals Teddy’s mother Sandy Alicia Silverstone was a patient at Auxolith, and is now comatose after undergoing medical trials with the company. This history fuels Teddy’s paranoia and shapes his distrust of the corporation.
Three days before the eclipse, Teddy bikes to work and is stopped by Casey Stavros Halkias, a local sheriff who used to babysit him. Their uneasy exchange hints at old tensions. Teddy later returns home and sees a news report confirming that Michelle is missing.
Michelle denies the alien claim but tries to negotiate her release. The confrontation grows heated, and Teddy slaps her after she challenges his logic.
Two days before the eclipse, Michelle tries to voice the truth again, but Teddy subjects her to an electroshock device, a torture that even Don finds troubling. He interprets Michelle’s high tolerance as a sign of higher status among Andromedans, further hardening his resolve. A brief flashback shows how Michelle covered up the incidents that left Sandy and other patients in comas, intensifying Teddy’s fixation on the corporation.
One day before the eclipse, the trio sits down for dinner. Michelle counters Teddy’s theories about an Andromedan link to dying bees, and the argument escalates until he lunges across the table and attacks her, leaving her stabbed with a fork.
Casey arrives to investigate Michelle’s disappearance, forcing Don to retreat with Michelle to the basement and keep her at gunpoint. Upstairs, Teddy and Casey confront painful memories of Teddy’s past—Casey admits he molested Teddy years earlier and tries to make amends, though the tension remains dangerous. Teddy then leads Casey outside to show him his apiary, while Michelle pleads with Don to call the police. Don, torn between loyalty and the fear of Teddy’s undertow, finally tells Teddy he’s sorry and that he loves him, only to shoot himself in the head, sending blood splattering over Michelle. Teddy and Casey hear the shot; in a frenzy, Teddy flings bees into Casey’s face and bludgeons him to death with a shovel.
Teddy returns to find Don dead, and Michelle reveals a plan to help Sandy by offering an Andromedan cure in a bottle of antifreeze. Teddy races to the hospital and uses the antifreeze to tamper with Sandy’s IV, though the attempt ends in tragedy, killing Sandy. He escapes before authorities arrive.
When Michelle confronts Teddy again, she finally acknowledges that she is an Andromedan empress who first arrived on Earth in the age of dinosaurs. Her people aim to reset humanity’s course, and the experiments on Sandy and other Auxolith patients were meant to advance humanity’s next evolutionary step. She urges Teddy to take her to Auxolith so she can contact the mothership.
Together they reach Auxolith and she leads him to her office, where he straps a homemade bomb to himself. Michelle has Teddy hide in a closet as she activates a device meant to reach the Andromedan mothership. The blast rips through Teddy; his severed head flies out, knocking Michelle unconscious.
Michelle awakens in an ambulance, escapes, and makes her way back to the office. She finds a hidden room full of corpses and the remains of others whom Teddy suspected might be Andromedans. She ultimately reveals she is indeed an Andromedan empress and teleports onto the mothership, reuniting with her people. The Andromedans declare Earth a failed experiment and destroy the planet by popping a bubble model of Earth. As Earth’s population dies, the world’s bees begin to slowly return to their habitats back on Teddy’s quiet, bee-filled prairie.
