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. God's Gardeners are devoted to preserving all plant and animal life, and they predict a disaster (The Waterless Flood according to the Gardeners, known by the readers to be Crake's viral pandemic) will radically alter the Earth.
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 flashback with the two main characters separately surviving the apocalypse described in the previous novel, both reminiscing about their time in the God's Gardeners religious movements and the events that led to their current positions.
Toby is a young woman who loses her family, blaming the corporations, and is forced to work in a low-quality burger joint. She soon encounters the unwelcome attention of the brutish manager of the chain who is depicted as grooming and assaulting women in his employ. Adam One, depicted as a self-proclaimed messiah but perceived by outsiders as a cult leader, saves Toby from the manager and takes her to the sanctuary of his rooftop garden. Toby becomes an influential member of the gardeners and encounters Ren, a child member of the gardeners.
Ren eventually grows up to become a trapeze dancer in the sex club Scales and Tails, and happens to be locked in a bio-containment unit in the club when the pandemic occurs. Similarly, Toby is barricaded within a luxury spa where she has begun to work following the gardener's raid.