After Earth is ravaged by a great religious war, an atheistic android architect sends two of his creations, Mother and Father, to start a peaceful, godless colony on the planet Kepler-22b. Their treacherous task is jeopardized by the arrival of the Mithraic, a deeply devout religious order of surviving humans.
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.
Using his mysterious new powers, Marcus rescues a group of Mithraic prisoners, while Mother discovers the serpent is not a maneater but an herbivore. Father works through his frustration over Mother’s decision to spare the serpent’s life by engrossing himself in his work project, the regeneration of an ancient android.
After the Trust uses Paul to strike back against Marcus, Mother confronts the Trust and threatens a coup. Meanwhile, on the run from Mother, Marcus has to keep his followers from losing faith as his powers suddenly disappear.
Mother struggles to keep the collective from falling apart as she struggles to lead while Sue resorts to prayer in her desperation to cure Paul. Meanwhile, Marcus and his followers are given new hope as they discover an ancient temple. But as Marcus investigates the temple’s secrets, Decima and the rest of his followers are made to answer for their sins.
As they try and fail to open the seed box, Sue and Paul realize they need Marcus’s help. Sue makes a plan to break Marcus out of the brig while Mother is distracted with the imminent birth of Tempest’s baby. But when Sue, Paul and Marcus finally open the seed box, they make 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.