After Earth is rendered uninhabitable, Androids Mother and Father start a new settlement and family with human embryos on the planet Kepler-22b. Twelve years later, only one child, Campion, remains, and the arrival of an Ark of surviving humans called the Mithraic presents a threat that Mother has no choice but to confront.
After a confrontation with Marcus, Mother discovers and takes five Mithraic children (Hunter, Tempest, Paul, Holly and Vita) back to her settlement. While Mother, Father and Campion, adjust to living with a new group of Earth-born children, Marcus struggles to survive alone on Kepler-22b.
After the Mithraic kids fall sick, Campion believes Mother is poisoning them and plans an escape. As Mother and Father attempt to prove otherwise, Marcus and Sue work to convince the other surviving Mithraic to mount a rescue of the children, desperate to get their son Paul back.
Determined to prove his utility to their family unit, Father tries to teach the children how to hunt some of Kepler-22b's mysterious creatures for food. Meanwhile, after the Mithraic make a stunning discovery that potentially fulfills one of their prophecies, a debate about how to proceed ignites a conflict between Marcus and Ambrose, their leader.
Under Marcus' command, the Mithraic set out on a deceptive path to rescue the children, and along the way, encounter a fellow survivor from the Ark. Back at the settlement, Campion and Paul bond during a hunting expedition with Father, Mother attempts to learn more about her origins, and Tempest's trauma continues to haunt her.
After reconnecting with her creator, Mother finds herself distracted by intense feelings she didn't know she was capable of, leaving the settlement vulnerable to Marcus, Sue, and the Mithraic's swift approach. As Campion continues to question his family's principles, the other children's loyalties are tested.
Struggling to maintain his clout as leader of the Mithraic, Marcus begins to make decisions that disturb his family, while Mother's ability to see him for who he truly is threatens his power and puts her in a precarious position. With Tempest on his side, a strong-willed Campion finds himself at dangerous odds with the Mithraic.
As Marcus continues to embrace his Mithraic devotion, Sue and Paul's distrust in him deepens. Meanwhile, Mother attempts to alleviate perceived malfunctions, Hunter works on a secret project with Father, and Campion and Paul devise an underground plan of their own.
Determined to keep the children safe, Sue grapples with whether or not she can trust Mother. Meanwhile, Tempest confronts her trauma, Hunter continues his attempts to restore Father, and when a new threat arises, the Mithraic begin to question an increasingly erratic Marcus.
Paul begins displaying troubling behavior that leads to a shocking revelation. Sue confides in Mother while Father battles unfamiliar human-like emotions. As Campion questions his place in his new family, Mother and Father uncover a distressing secret about Kepler-22b's native creatures.