Hunger is set three months after Gone.
When all kids in the FAYZ have wasted most of their food and let it spoil, Sam asks for a group of people to get on a bus to help pick plants out in the farmlands. A kid named E.Z. dies when he goes to the fields to pick cabbages as mutated worm-like creatures, called Zekes, attacked him.
Meanwhile, the character Duck unintentionally creates a whirlpool using his powers that suck him from his pool to an underground cave and discovers mutated blue bats. These taste disgusting to humans, but can be fed to the Zekes in exchange for children being allowed to pick cabbages without being attacked. Fueled by a widespread prejudice against people with powers, especially after he almost got sucked into a whirlpool made by Duck because he bullied him around and angered him, Zil creates the "Human Crew", an organization that discriminates against these "freaks".
Caine wakes up from a three-month coma and tells Diana to bring Computer Jack back to Coates so they can take over the nuclear plant in order to control the town's electricity. After ending up losing all electricity Caine mentally receives a message from the gaiaphage telling him to bring it a uranium rod from the plant and realizes it may be controlling him. Lana has also been receiving messages from the gaiaphage and attempts to blow up the mine shaft, but she fails, falling under the gaiaphage's control.
Edilio Escobar, a student from Perdido Beach, travels to the mine shaft in order to destroy it, along with another girl named Dekka who has the ability to defy gravity in small spaces. He is shot by Lana, who is under the control of the gaiaphage. It is revealed that the gaiaphage plans to use Lana's powers, along with a uranium rod from the nuclear plant, to create a new, near-invincible body for itself. Astrid determines that the gaiaphage was created by the accident at the nuclear plant 15 years ago, and that the accident may also be the cause of her peers' supernatural powers.
Sam and Duck Zhang, who can control his density, travel to the mine shaft in order to fight the gaiaphage. Caine uses his powers to bring a uranium rod to the mine shaft, but, upon seeing his love interest Diana Ladris injured by Drake, throws the rod at his chest, knocking him into the mine shaft and collapsing its entrance. Duck creates a hole in the ground leading to the gaiaphage and is then thrown by Caine into the hole. While falling, Duck becomes heavier than a mountain and smashes into the gaiaphage, dragging the creature down to the bottom of the barrier surrounding the FAYZ but dying in the process.
Lana heals Sam. Orc and Howard keep the town kids from hanging Hunter and save Astrid and Little Pete. The book ends on a cliffhanger when the readers realize Brittney, a girl buried in the plaza, is still alive.