Cellular biology professor and former U.S. Army soldier Lena is under interrogation. She was part of an expedition to an anomalous zone known as the "Shimmer", but she was the only one to return.
The Shimmer emerged three years prior from a meteor that landed in a lighthouse in the St. Mark's National Wildlife Refuge in Florida, and it is gradually expanding and increasing its boundaries. Many exploratory expeditions were organized, but only Lena's husband Kane returns home after a year of absence.
Kane cannot explain where he was and how he came back, and his condition quickly deteriorates. Lena calls an ambulance, but she and Kane are intercepted by security forces and taken to a secret facility.
As Kane is put in intensive care, psychologist Dr. Ventress prepares a new scientific expedition into the Shimmer, and Lena joins her. Three other women participate in the expedition: Cass, a geomorphologist; Anya, a paramedic; and Josie, a physicist.
Communication equipment does not function within the Shimmer's territory, and the expedition encounters unusually mutated plants and animals. Josie is attacked by an albino alligator with several concentric rows of teeth.
At an abandoned military base, the group finds a video message from Kane's expedition, in which Kane cuts open another soldier's abdomen with a knife to reveal slithering intestines. The group finds the soldier's corpse, which has turned into an overgrown colony of lichens.
At night, the base is attacked by a mutant bear that drags Cassie away, and Lena later finds her mutilated body. Within an abandoned village, Josie studies plants that have taken on a humanoid form, and theorizes that the Shimmer functions as a prism, distorting and transforming everything that falls within its boundaries—including the expedition members' own DNA.
Anya, overcome with paranoia after watching her fingerprints change, disarms the other members and ties them to chairs, and accuses Lena of murdering Cassie. The mutant bear returns and lures Anya away by emitting a cry for help in Cassie's voice. The bear kills Anya, while Josie frees herself and shoots the bear.
Ventress leaves the group and heads for the lighthouse, the center of the Shimmer. Josie believes Cassie's dying mind was "refracted" into the bear, and then allows herself to "refract" into a humanoid plant to avoid a similar fate.
Lena follows Ventress to the lighthouse, where she discovers Kane's remains and a videotape. In the footage, Kane leaves an instruction to find Lena before killing himself with a phosphorus grenade. After the explosion, a doppelgänger of Kane steps into frame.
Within the hole created by the meteor, Lena finds Ventress, who explains that the Shimmer will eventually swallow everything. Ventress then disintegrates into a shimmering cloud that absorbs a drop of blood from Lena's face and changes into a faceless, shimmering, humanoid being that mimics Lena's movements.
Unable to escape the creature, Lena tricks it into igniting one of Kane's leftover grenades as it transforms into her doppelgänger. Lena flees the burning lighthouse and the Shimmer dissipates.
Lena visits the Kane doppelgänger, and asks if he is really Kane, which he doubts. He asks if she is Lena, but she does not answer. They embrace and their irises shimmer.
