In the near future, an extinction level event rocks planet Earth, and an underground bunker is activated. Its program is designed to repopulate the Earth. A robot, called Mother (voiced by Rose Byrne), initiates her program and grows a human embryo into a baby, which it then raises into childhood. The young girl asks Mother why she's the only child, and Mother tells her she needs some time to learn about raising children. Many years later, a teenage Daughter (Clara Rugaard) lives with Mother in the bunker. Mother gives Daughter lessons on ethics and morals in preparation for a looming exam. Later, the power goes out in the facility, taking mother out with it. Daughter goes to find the source of the trouble and captures a mouse that led to an electrical malfunction. Daughter thinks the mouse means there is life outside the bunker, but Mother believes the mouse could be a carrier for disease and incinerates it. Still curious, Daughter begins investigating, dons a hazmat suit, and starts poking around the facility's airlock. Once there, she hears a Woman (Hilary Swank) wounded badly from a gunshot and crying out for help from outside. Daughter opens the lock, gets the Woman to put on a hazmat suit, and leaves her hidden in the airlock as Mother quickly arrives. Mother insists that contagion outside the bunker would kill her, and then tells her that she take her exam immediately.Daughter heads back to the airlock to find the Woman asleep. She finds a gun in her bag and takes it, then gives her water - when the Woman takes her mask off to drink it, Daughter realizes there must not be contamination outside the bunker. While Daughter goes to get medical supplies, Woman sees Mother and reaches for her gun but finds it missing. When Daughter returns, Woman demands the gun saying that Mother is just like "her friends outside". Woman shoots at Mother but is quickly overpowered and taken to the infirmary, where the Woman refuses Mother's medical aid. Daughter confronts Mother about the supposed toxicity levels outside, and Mother admits that she lied to keep her safe and is not like the robots who attacked the Woman. Mother tells Daughter they can help any other survivors but they need the Woman to cooperate.Daughter tries to convince Woman that Mother isn't bad, but the Woman tells her she's seen the horrors the robots have inflicted. Daughter asks Mother if she knows other robots, but Mother says she doesn't remember ever not being in the bunker. Woman's conditions worsens, and Mother says she'll need surgery. Woman refuses to let Mother operate, so Daughter volunteers. Mother guides her through the surgery, which is tough but successful. After the surgery, Woman is kinder to Daughter. Woman confesses she was on a food run with her brother when the robots attacked. Her brother distracted them and she got away, never making it back to the mines where her people live. Woman tells Daughter she should go with her, but Mother interrupts and tells Daughter to take her exam. Mother confiscates Woman's bag, and when Daughter asks why, Mother says that the bullet they pulled from Woman matches the one she fired at Mother with gun she brought in - not a gun robots use. She was shot by another human. Mother thinks she's dangerous.Daughter completes the exam. When she passes, Mother allows Daughter to select a new embryo to add to their family. Daughter confronts Woman about lying, but Woman asks her if she saw the bullets with her own eyes. She breaches security and checks the bullets herself, and finds they don't match. She goes through more records and learns that Mother had raised several other children before her, and finds human remains in the incinerator. Daughter returns to Woman and tells her she believes her. Woman insists they go back to the mine, but Daughter wants to wait for her currently gestating new brother and says they just need to stay one more night. Before she can, Mother, who was eavesdropping on the escape plan, locks her in a room and goes Woman, demanding the location of the mines. Daughter breaks out, setting off alarms, and in the melee Woman is also able to escape. In order to escape, Woman holds a knife to Daughter's throat which forces Mother to open the airlock, and they escape. Daughter is angry, but goes along with Woman.Outside, they narrowly avoid some other robots, which appear to be planting crops and purifying the air. Mother says that before the robots the Earth was virtually uninhabitable. When they reach Woman's home, Daughter learns that Woman actually fled the tunnels years before and has been living alone for a long time. Daughter wants to find them, but Woman says they had devolved into madness. Daughter is horrified she left her brother and flees to go back to the compound - Woman refuses, too scared. She encounters a fleet of robots who let her pass. She enters the compound, taking an axe for protection, and finds Mother and her brother. Mother explains that she was created to protect humanity, and when she saw the human race destroying themselves, she took action to create a new world that humans would flourish in, and raising humans who are ethical. Mother lets Daughter hold her brother, and when Daughter attempts to flee, Mother chases her. Daughter aims a gun at her but Mother reveals that she is every robot on Earth - all one consciousness. Daughter pleads with Mother to let her raise the brother on her own, and Mother acquiesces, letting Daughter shoot her, destroying that body.The Woman is alone when Mother comes to her and implies that she was only alive and free to serve her plans, and kills her. At the compound, the Daughter sings a lullaby to her brother, then walks into the embryo room - now the mother to them all.