After Earth is torn apart by religious differences and the human race teeters on the edge of extinction, an atheistic android architect sends two of his creations, Mother and Father, to start a peaceful, godless colony on the planet Kepler-22b. Raised by Wolves follows Mother and Father as they attempt to raise human children in this mysterious virgin land, a treacherous and difficult task that's jeopardized by the arrival of the Mithraic, a deeply devout religious order of surviving humans. As the androids make contact with this zealous and dangerous people, they struggle to control the beliefs of their fiercely self-determining children.
Androids Mother and Father flee an uninhabitable Earth to settle on the planet Kepler-22b and start a family with six human embryos. Twelve years later, only one child, Campion, remains. As Mother and Father begin to malfunction, the arrival of the Ark of Heaven – a spacecraft carrying the Mithraic, a religious order of surviving humans – presents a threat that Mother has no choice but to confront.
After her confrontation with Marcus and the Mithraic, Mother takes five of their Earth-born children – Tempest, Paul, Hunter, Holly, and Vita – to live on the settlement. As she and Father attempt to put the shaken newcomers at ease, Marcus struggles to survive alone on Kepler-22b. Meanwhile, Campion tries to ingratiate his new friends but begins to question Mother's motives.
When the Mithraic kids fall sick with a mysterious illness, Campion suspects Mother is poisoning them and plans an escape. As Mother and Father attempt to prove their good intentions, Marcus and Sue, desperate to get their son Paul back, work to convince the other surviving Mithraic to mobilize a rescue party for the children.
Father tries to teach the children how to hunt some of Kepler-22b's mysterious creatures for food. Meanwhile, the Mithraic make a stunning discovery that potentially fulfills a Mithraic prophecy, and a debate about how to proceed ignites a conflict between Marcus and the Mithraic leader, Ambrose.
Marcus moves forward with a plan to rescue the Mithraic children, but first he has to find them. Back at the settlement, Campion and Paul bond while on a hunting expedition with Father, and Mother attempts to learn more about her origins.
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 worries he may no longer have her and Paul's best interests at heart. Meanwhile, Mother experiences what she believes to be malfunctions, and Hunter works on a secret project with Father.
Sue is determined to keep the children safe, and in doing so, struggles with whether or not she can trust Mother. Meanwhile, a new threat arises and an increasingly erratic Marcus causes the Mithraic to question their leader.
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.
While Mother, Father, and the children face hostility from their new atheist collective, Marcus sets out to fill the walls of an ancient church with Sol's worshippers.
While the collective is tasked with hunting down the serpent, Mother is left to reconcile complicated emotions. Convinced that it will aid his cause, Marcus sets out to find the creature before the atheists do.
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Upon learning that the serpent is nonviolent, Mother fiercely protects it, while Father busies himself with the regeneration of a new android. Endowed with mysterious new powers, Marcus grows his congregation.
After the Trust uses the children to strike back against Marcus, Mother takes matters into her own hands, and Father has a breakthrough.
Sue resorts to prayer in her desperation to cure Paul, Father's project takes on new life, and hope is briefly renewed for Marcus and his followers.
While Mother is distracted by the imminent birth of Tempest's baby, Sue and Paul make plans to free Marcus and plant the tree – but are met with a horrifying discovery
A reeling Marcus and Paul join forces with Mother to disarm the newly weaponized serpent before it wreaks unimaginable havoc.
Grandmother reveals her own agenda, Marcus seeks revenge, and Mother sets out to neutralize the serpent – but is leveled by the fallout.