At the U.S. government's Area X facility on a southern coast, cellular biology professor and former U.S. Army soldier Lena is under interrogation. Previously she was part of an expedition to an anomalous zone known as "the Shimmer", but was the only one to return. The Shimmer emerged three years prior from a meteor that landed in a lighthouse near the facility, and 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, seems to be in a permanent daze, 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, with Lena joining her. Three other women participate in the expedition: physicist Josie Radek, geomorphologist Cassie "Cass" Sheppard, and paramedic Anya Thorensen.

 

The group enters the Shimmer, and Lena has a brief vision of her affair with her co-worker Dan. When the group awakes, they find their communication equipment does not function and they have no idea where they are. They conclude that three to four days had already passed since they entered, but they do not remember anything after entering the Shimmer. They encounter unusually mutated plants and animals, and Josie is attacked by an albino alligator with many rows of shark-like teeth. At an abandoned military base, the group finds a video message from Kane's previous expedition. It shows Kane using a knife to cut open the abdomen of another soldier to reveal his 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 Cass away, and Lena later finds her mutilated body. Within an abandoned village, Josie studies plants that have taken on a human-like form, and theorizes that the Shimmer functions as a prism for DNA, distorting and transforming everything that falls within its boundaries, including the expedition members' own bodies. Anya, overcome with paranoia after watching her fingerprints change, disarms the other members and ties them to chairs, and accuses Lena of murdering Cass. The bear returns and lures Anya away by emitting a cry for help in Cass' voice. The bear kills Anya, while Josie manages to free herself and shoots the bear.

 

Ventress leaves the group and heads for the lighthouse, the center of the Shimmer. The next morning, Josie convinces Lena she is right about the refractions within the Shimmer. Lena comments that she checked her blood the previous night and that the Shimmer is in her. Ventress wants to face it, because she has cancer and has nothing to lose. Lena wants to fight it because it took her husband, whom she now believes accepted the suicide mission into Area X because she cheated on him with her coworker. Josie walks away, with Lena calling after her. Josie believes Cass' dying mind was "refracted" into the bear, and allows herself to "refract" into a human-shaped 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 commits suicide with an incendiary grenade, but after the explosion, a doppelgänger of Kane appears. Lena descends into the hole created by the meteor and finds Ventress, who tells her the forces at work will spread to encompass everything. Ventress disintegrates into a glowing nebulous structure that absorbs a drop of blood from Lena's face and creates a humanoid entity that mimics nearly all of Lena's motions and eventually transforms into an identical copy of her that begins copying her thinking. Lena exploits its mimicking behavior by having it copy her suicidal self-destructiveness before setting an active phosphorus grenade in its hands and fleeing. The creature makes no attempt to follow as it is set ablaze by the grenade. Now on fire, and having seemingly internalized Lena's self destructive urges, the creature affectionately touches Kane's burned body before crawling back into the hole and igniting the core of the lighthouse. Flames fully engulf the lighthouse, the various constructs in the area collapse, and the Shimmer fades away.

 

Lena is told by her interviewer that Kane's condition rapidly improved after the Shimmer vanished, and that he is now not only healthy again but more lucid than at any other time since his apparent "return". Lena visits Kane, and asks if he is really Kane; he replies, "I don't think so”, possibly suggesting that he is a doppelgänger. He asks if she is Lena, and she does not answer. Kane's (possible) doppelgänger embraces Lena and their irises shimmer.

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