The Year of the Flood details the events of Oryx and Crake from the perspective of the lower classes in the pleeblands, specifically the God's Gardeners who live in a commune at the Edencliff Rooftop Garden. God's Gardeners are a religious sect that combines some Biblical practices and beliefs with some scientific practices and beliefs. They are vegetarians devoted to honoring and preserving all plant and animal life, and they predict a human species-ending disaster, which they call "The Waterless Flood". This prediction becomes true in a sense, as Crake's viral pandemic destroys human civilization. God's Gardeners have their own set of saints, all honoured for their environmental activism, such as Saint Dian Fossey and Saint Rachel Carson.
The plot follows two characters, Toby and Ren, whose stories intertwine with each other and, at points, with major characters from Oryx and Crake. Much of the story is told through flashbacks with the two main characters separately surviving the apocalypse described in the previous novel, each reminiscing about their time in the God's Gardeners religious movement and the events that led to their current situations. Atwood uses third-person narration for Toby's accounts and first-person narration for Ren's.
Toby is a young woman who loses her parents under tragic circumstances that may or may not be due to the corporations and is forced to live off of the grid in a shady meat burger joint working as a meat barista at SecretBurgers. She soon encounters the unwelcome attentions of Blanco, the psychopathic manager of the chain, who has a reputation for sexually assaulting and murdering the women in his employ. Toby is able to escape when a group of God's Gardeners arrive at the restaurant. She follows them to the rooftop garden, where she finds her former colleague Rebecca.
The leader of God's Gardeners, Adam One, is admired as a charismatic holy man within the group, but he is perceived by outsiders as a cult leader. The novel is filled with sermons and hymns Adam One gives to the religious sect. Although she is skeptical, finding it difficult to follow the theology and follow the religious traditions, Toby becomes an influential member of the gardeners. She even rises to the official position of an Eve. Within the sect Toby encounters Ren, a child member of the gardeners.
Ren joined the God's Gardeners when her mother, Lucerne, left her HelthWyzer scientist husband after falling in love with Zeb, a member of the sect. Ren grows up in the religious sect, befriending Amanda, until Lucerne decides to go back to the Compounds. Ren goes to school, where she meets Jimmy (Snowman) and Glenn (Crake), who is particularly interested in the God's Gardeners. Later, Ren enrolls in a Dance Calisthenics courses at the Martha Graham Academy, until Lucerne is unable to pay and she drops out. Eventually, Ren becomes a sex worker and trapeze dancer in the sex-club Scales and Tails, part of SeksMart. Here, Ren happens to be locked in a bio-containment unit in the club called the Sticky Zone when the pandemic occurs. Amanda rescues Ren from the club.
Blanco is able to find out where Toby is and raids the Gardeners. Toby is able to flee, relocating to the AnooYoo spa. In fear, she changes her outward appearance through cosmetic surgery to hide from Blanco. Toby barricades herself in the luxury spa as the plague spreads, utilizing the skills of foraging she learned with the God's Gardeners to survive.
Blanco participates in the televised game Painball, where teams of criminals try to kill each other in the surrounded arena. Blanco and three companions escape the Painball forest to find Toby at the spa. They capture and torture Ren and Amanda. Toby is able to shoot one of the criminals and free Ren, but the others escape with Amanda. Both Toby and Ren come together to search for Amanda. Toby poisons Blanco, and she and Jimmy incapacitate the two criminals. The novel ends much like the ending of Oryx and Crake, with the remaining survivors witnessing an unknown group approach, carrying torches and playing music.
