Seven-year-old Chloe Lewis, Lexy Kolker, has spent her entire life inside a dilapidated house, forbidden to step outside by her father Henry, Emile Hirsch who warns that “the bad men” will harm them if she ever tries to leave. Chloe longs for the outside world and for a maternal figure she never knew, Mary, while Henry trains her in social graces so she can one day blend in with the neighboring Reed family.
From the shadows, Chloe notices unsettling signs—Henry bleeding from his eyes after fits and visions of a woman in her closet. She learns about abnormals, people with extraordinary abilities who are hunted by the government’s Abnormal Defense Force (ADF) and kept in a facility beneath Madoc Mountain.
One day Chloe escapes the house and discovers she can manipulate another person’s mind, a power that surfaces under pressure. The elderly ice-cream truck driver who stops by reveals he is Chloe’s maternal grandfather Alan, Bruce Dern, and that he believes Mary may still be alive.
Chloe’s realization comes into sharper focus when she sees that the woman in her closet is Mary, who is being held at Madoc Mountain. The truth confirms that Henry and Alan are abnormals, their eyes bleeding as a sign.
To secure Chloe’s future, Henry uses time-bending powers to compress seven years into a matter of months, so the world outside hardly ages while he keeps her inside. He then ferries Chloe to the Reed family with a substantial sum of money, but the Reed matriarch Nancy Reed, Michelle Harrison, rejects them and alerts the ADF. Chloe, using her mind-manipulation ability, turns the situation to her advantage and causes Nancy to be killed by the pursuing agents.
With Nancy out of the way, Chloe begins to help Mary escape from Madoc Mountain, but ADF Agent Cecilia Ray, Grace Park, arrives and reveals she knows the truth about their family, warning that a drone strike will be ordered if violence escalates. Ray destroys Alan and mortally wounds Henry before Chloe defeats Ray.
In a final act of defiance, Henry delays the ADF long enough for Mary’s escape, then slows time and carries Chloe out of the house as it is destroyed by a Hellfire missile. Henry succumbs to his injuries, leaving Mary to arrive with the power to fly and finish off the remaining agents. Mary promises to keep Chloe hidden, but the fearless girl insists they should live openly, wherever they choose. Mary agrees and, with Chloe, flies into the sky, leaving the future—for now—unwritten.