At "Area X", a government facility on the southern coast of the US, Lena, a cellular-biology professor and former soldier, is in quarantine. She undergoes a debriefing about a four month expedition into an anomalous iridescent electromagnetic field called "the Shimmer" from which she and her husband Kane are the only survivors.
In flashback, Lena's husband, an Army Special Forces soldier, appears in their home after having gone missing on a mission nearly a year ago. He remembers nothing of that time and suddenly becomes very ill. A government security force intercepts Kane's ambulance and transports him and Lena to Area X, near where the Shimmer had begun to spread three years earlier. A psychologist, Dr. Ventress, explains that military teams, including Kane's, have ventured into the Shimmer to attempt to reach the lighthouse where the phenomenon first appeared. Kane is the only person to have ever returned from an expedition. Lena volunteers to join Ventress on a research expedition consisting of two scientists, Josie and Cassie, and a paramedic, Anya.
Guidance technology fails, the expedition members realize they are unable to remember extended stretches of time, and a mutated alligator attacks Josie. The team rescues her and learns that the alligator shows signs of being hybridized with a shark. At an abandoned military base, the team discovers evidence of Kane's expedition along with a memory card left for them. A video on it shows Kane cutting open the stomach of a fellow expedition member while he was still alive, revealing that his intestines have begun to wriggle in a worm-like manner. That night, the base's perimeter fence is torn open, prompting everyone to investigate. Suddenly, a mutated bear drags Cassie away; the following morning, the team finds one of her boots. Lena searches further, alone, and she discovers Cassie's mutilated corpse. Lena returns to the team and reports that Cassie has died.
As the team continues toward the lighthouse at the center of the Shimmer, they find a decayed settlement with human-shaped plants outside it. Josie says she thinks the Shimmer is acting on organisms in the manner of a prism, distorting and refracting DNA in the same way that a prism refracts light. The expedition members realize they are slowly changing as well. That night, Anya descends into a psychotic state, attacking and restraining the other team members. As she is threatening them, Anya hears what sounds like Cassie crying for help outside and investigates. The bear that killed Cassie enters the house, its roar imitating Cassie's dying screams. It kills Anya and attacks Lena before Josie can shoot it dead.
Ventress leaves Lena and Josie to complete the journey while she still can. Josie muses that she doesn't want to go on and begins to grow flowers from her body. She walks away from Lena and disappears among the human-shaped plants. Lena reaches the lighthouse and goes inside, finding an incinerated corpse, a video-camera and a hole in the floor. Footage on the camera shows Kane ranting about the Shimmer's effects on him. He urges the cameraman to find Lena, then commits suicide with a white-phosphorus grenade, after which a doppelgänger of his walks into view.
Lena descends into the hole in the floor and finds Ventress, who has also begun to mutate. Ventress tells Lena the forces at work will eventually encompass "everything", before disintegrating into a fiery nebulous structure that absorbs a drop of blood from Lena's face and creates a humanoid being. Lena attempts to escape the lighthouse but the humanoid stops her, mirroring her movements. Lena passes out which the humanoid does as well. Somehow, Lena's head bleeds streaming down her cheeks as soon she wakes up. Lena turns around to the humanoid and catches it copying her. She give it a grenade and holds its other hand. The humanoid gradually transforms into an identical copy of her. Lena opens the grenade, and activates it which it explodes causing the humanoid to shine and transform back into its official self and the humanoid watches Lena run outside and leave it alone. The being is set ablaze, flames engulf the lighthouse, the various constructs in the area collapse, and the Shimmer dissipates to nothing.
Lena's debriefing concludes, and she reunites with Kane, who has recovered rapidly with the Shimmer having ceased to exist. She asks him if he is the "real" Kane, to which he replies, "I don't think so." He asks her if she is Lena, but she does not answer him. The two embrace, and their irises shift to Shimmer colors.
- Natalie Portman as Lena
- Jennifer Jason Leigh as The Psychologist
- Gina Rodriguez as Anya Thorensen
- Tessa Thompson as The Surveyor
- Tuva Novotny as The Linguist
- Oscar Isaac as Lena's husband