Connie Temple, Sam and Caine’s mother, had been working on her laptop when suddenly she was transported to the beach. All around her, other adults found themselves transported from their lives to places outside of Perdido Beach. In the months since the appearance of the Bowl, as it became known to the outside world, the military set up a base and began monitoring it. They are all shocked to learn that after months of identical readings, something appears to have changed. The energy waves the Bowl gives off appear to be weakening.
Within the FAYZ, things have also changed in the past three months. Since throwing her brother, Petey, to mutant carnivorous insects and watching him disappear, Astrid has been living off the grid. Alone along the wall of the dome, Astrid has lost her faith in God but found confidence in her own ability to survive. Still terrified of having to face Drake, she has learned to shoot a rifle and take care of herself.
Sam and a group of kids that number just over 100 have set up a new community along Lake Tramonto. The months of peace have brought a sense of optimism to the children, but Sam finds himself growing bored. Diana, pregnant with Caine’s baby, is worried at how fast her pregnancy is progressing. She is only four months along, and yet she can feel the baby strongly kicking. She can also sense that it is a mutant and is growing more powerful every day.
In Perdido Beach, King Caine holds court to determine the punishment for Cigar, a boy who accidently killed another teen during a fight. Cigar has never caused problems before and is on Quinn’s crew of fishermen, but Caine feels the penalty should be severe. He orders Cigar to suffer an entire day at the hands of Penny, a mutant who can torture people by creating incredibly real hallucinations.
While all this goes on in and around the dome, Pete Ellison, Astrid’s autistic brother, finds himself living in a reality outside of both worlds. In this place, he is free of the tortures of his autistic mind. At first content to be in this new place, Pete eventually grows bored. He notices strange avatars, symbols with squiggles inside, floating around him. He decides to try and play a game with them, but when he touches one, it breaks apart.
Back within the FAYZ, a little boy’s body is twisted and mutilated until he dies. When Pete tries to play with another avatar, a young girl’s face melts into her chin, and her body is mutated into a kind of log. Finally, Pete tries something different and ends up transforming a girl named Taylor into gold. When she tries to transport herself to Lana for healing, her body gets stuck in a car. Her hand and legs are amputated, without blood.
Quinn leaves work to retrieve his friend Cigar from Penny. He is horrified to discover Cigar has gouged out his eyes and cut his wrists in response to Penny’s visions. He takes the boy to the healer, Lana, but she can only regrow two marble-like eyes that do not completely restore his sight. Quinn threatens to go on strike with his fishing crew unless Caine evicts Penny from the community.
Meanwhile, Astrid has noticed something strange about the dome: It is growing dark. She sets off to tell Sam about her findings and hopes to perform an experiment to show how long it will take the darkness to cover the FAYZ. When she arrives at Lake Tramonto, she waits for Sam in his bed. Unaware of her presence, he is surprised when he crawls in and she begins kissing him.
Where Astrid had previously abstained from sex because of her faith, she now initiates intimacy with him and the two make love. The following day, she tells him her theory that the FAYZ is going dark, something that terrifies Sam. Later, she sneaks away in an effort to warn the community at Perdido Beach about the coming darkness. But the darkness spreads through the dome at an increasingly faster rate, and she loses her way in the desert before she can deliver the message.
Drake has spent the past months below the earth with his god, the gaiphage, waiting for orders as to what he should do next since Pete disappeared. The gaiphage wanted Pete dead. Now the evil entity senses it can use Diana’s baby in order to be born again into this world.
It sends Drake above ground to find her and bring her back. He eventually succeeds in kidnapping her. Sam sends Jack, Orc and Dekka to try and save her, but Drake cuts Jack’s neck open with his whip hand. Orc carries him back to the lake for help while Dekka follows Drake and Diana.
Penny tricks Caine into visiting her and then drugs him so he cannot use his telekinetic powers to hurt her. While he is unconscious, she encases his hands in cement so that he will remain helpless. As the FAYZ becomes completely dark, she leads King Caine out to the town square and forces the kids to mock him. Albert, the boy whose organizational skills really run the community, sees the crowds and the encroaching darkness and flees Perdido Beach for a well-stocked, isolated island where he has hidden missiles Sam had previously found.
The kids at the beach do not rally around Penny. They need Caine and his powers to protect them from the coyotes and other beasts that rule the night inside the FAYZ. Penny is eventually driven off, and Quinn is made temporary leader while they try to release Caine’s hands from the cement.
Astrid meets up with Cigar, who has wandered away from Perdido Beach. She realizes with his new eyes he is able to see things in other dimensions. He is able to see Pete. She tries to communicate with her brother but Cigar’s connection to Pete is intermittent. When coyotes attack Cigar, Pete destroys them with his finger. But later, when the boy is attacked by flesh eating worms, Pete does not help him.
Pete reaches out to his sister; he is able to communicate with her on a limited basis. He shows her how he had used a power from inside his body to create the dome. Without his body, he is unable to control it anymore. The barrier had been made of the gaiphage, which used it as a way to be reborn, but now it needs a body. Astrid’s brain begins to scramble from Pete’s touch, so he breaks the connection and leaves her.
Outside the dome, Connie becomes aware of the military’s plan to detonate a nuclear bomb beneath the dome to try and destroy it. She is terrified the explosion will kill the children inside. She and a friend rally other parents and the news media to try and stop the detonation.
Penny is led by the gaiphage to its lair where she meets up with Drake and Diana. As Diana goes into labor, Brianna arrives and shoots Penny and Drake, who has transformed into his alter ego, Brittany. Brittany/Drake cannot die, but is distracted when Brianna shoots off her head.
Brianna helps to deliver the baby. Although Diana begs her to take the baby out of the tunnel, the gaiphage tricks Brianna into giving it the child. The green substance that makes up the gaiphage enters the baby through her nose and mouth, taking possession of her. It heals Penny’s wounds before settling in to nurse. Brianna flees to find Sam and tell him what happened.
Sam finds Astrid in the desert. The two of them make their way to Perdido Beach, hoping to find help to fight the gaiphage. Lana and Caine both sense that the gaiphage has successfully taken a human body and is coming for them. Astrid knows the gaiphage wants to break open the dome and enter the real world. The children set off in the dark to stop it.
As they battle Drake, Penny and the gaiphage (now a toddler,) the military’s bomb explodes. Sunlight streams in, but the barrier doesn’t break. Sam recognizes the face of his mother by the barrier, but he cannot stop fighting the gaiphage. He turns his laser-like beams on the toddler, who is engulfed in flames, but is unhurt by them.
The gaiphage, Diana and Drake run away once they realize the barrier is still in place, only transparent. As the outside world begins to gather around the dome, the children know they cannot stop the adults from judging them for what they see, but they also know they do not have time to waste worrying about what will happen if they are ever free from the dome. They cannot give up the fight to stop the gaiphage.