Mina, an American immigrant working in a pet shop in Galway, Ireland, is struggling to come to terms with the death of her mother, which she accidentally caused 15 years ago, and is also estranged from her twin sister, Lucy. She follows an elderly woman, Madeline, to a bunker-like building called “The Coop,” where she meets two other residents, Ciara and Daniel. Madeline explains that a mysterious entity called “The Watchers” watches the group every night through the mirrored windows of the Coop.
Madeline explains the rules to Mina: At night, the Watchers kill everyone outside the Coop, and no one is allowed to enter the Burrows, the underground tunnels where the Watchers take refuge during the day, because they hate sunlight. Ciara’s husband, John, left the Coop a few days ago and has not returned. Daniel helps Mina explore the burrow, where he unearths several items, including a video camera and a bicycle, and narrowly escapes the guards. That night, John appears at the chicken coop, but Madeline won’t let him in. Madeline returns the items to the burrow to appease them.
As winter sets in, the groups begin to become hostile towards each other. Daniel locks Mina and Madeline out of the chicken coop one night, forcing them to take refuge in the woods. They witness the Guardians, human-like creatures who mimic the henhouse’s inhabitants and react angrily to Madeline and Mina’s absence. The pair return to the henhouse, where Madeline explains that the guards are shape-shifting fairies trying to learn how to mimic humans. The guards storm the henhouse. Mina discovers a video diary of Professor Rory Kilmartin, the inventor of the henhouse. The video ends with him climbing into the henhouse and killing the captured guards and himself. The next day, the group follows the professor’s instructions and has Darwin guide them to a river at the edge of the forest. On the way, Madeline shows them a stone marker and explains that humans fought with the fairies, lost their wings, and were driven underground and trapped in the forest. She visits Ciara and shows her a photo of her, revealing that Madeline was the professor’s late wife. Her “Madeline” is a security guard that the professor captured.
When the real Ciara arrives at the house, it turns out that Ciara is Madeline in disguise. Madeline transforms, knocks Ciara unconscious, and attacks Mina. She explains that she was ostracized among the Guardians due to her ability to walk during the day, and plans to kill and replace Mina. Mina reveals that Madeline is half-human and convinces her to let go of her hatred for humans, telling her that there may be others like her. Madeline begins to sprout feathers and leaves.
Mina later reconciles with her sister, Lucy. Meanwhile, Madeline was watching over Mina in the form of a human child.