The film begins with Lena teaching at a university; she is a cellular biologist. We learn that her husband Kane hasn't returned from a mission for over a year. But out of the blue he walks into their home, but he is out of sorts, and begins to cough blood and an ambulance takes him to a hospital; that is before it is stopped by a government security force who takes them to an area dubbed, "Area X." It is the headquarters for the study of "The Shimmer," an anomaly that appeared three years prior and continues to grow. Kane has gone into a coma and Lena is offered to opportunity to find out what happened to him by going into The Shimmer with Dr. Ventress, a government psychologist, and a small team of scientists and a paramedic.
When they go in they seem to lose their sense of time, and they discover that animals and plant life have transformed into something new, some of it very dangerous. The group loses one of its members, Cass when a mutated bear eats her and runs off with her body. Anya, a paramedic in the group, becomes paranoid and ties the other members of the team up wanting answers. But when she hears Cass crying out for help she goes to her, only to be met by the mutated bear which has mimicked the horrifying sound of her death. The bear kills Anya before Josie, a scientist in the group, is able to shoot and kill it. The group is in disarray and Ventress decides to push forward to find the source while Josie is determined to become part of "The Shimmer," and somehow joins herself to it; she mutates into a human version of flowers.
Lena left on her own pushes forward in order to destroy whatever it is that is causing the anomaly of "The Shimmer." Once she gets to the lighthouse, the epicenter of the event, she finds a video camera that reveals that Kane, her husband has committed suicide with a white phosphorus grenade. We then see a humanoid entity transform into an exact replica of Kane. Lena then finds Ventress in a burrowed hole beneath the surface before the doctor disintegrates and is absorbed by another humanoid entity, which follows Lena out of the hole, mimicking her every move. Lena uses this mirroring to her advantage by placing a phosphorus grenade in the hand of the entity and running away. It explodes and the entity dies, along with it "The Shimmer" begins to erode.
Back at the lab Lena is brought to see the replica version of Kane. She knows it isn't him, but it knows who she is and hugs her as the film goes to black.
