To the outside world, the children inside the now transparent dome that makes up the FAYZ (Fallout Alley Youth Zone) are dangerous. They watched as Sam burned Gaia, whom they perceived as an innocent toddler. They have read stories written by the surviving children about the murders, hunger and terror they have experienced. The names Caine and Drake are mentioned in a lot of their stories. Some on the outside believe the entire dome should be nuked. Others call for the children to be imprisoned, if the dome ever comes down.
Diana is now a prisoner of Gaia, the twisted child she gave birth to who was then possessed by the gaiphage. Gaia, now a little girl of about 10, was wounded in the battle with Caine and Sam, but because she is able to draw on the powers of the mutants within the FAYZ, she is slowly healing from her burns.
Diana learns that Gaia is nearsighted, and that her powers are more limited now that she is in a human body. Gaia uses the powers of the mutants she has connected with, including Sam, Caine, Brianna and Lana. If she kills them, she loses the ability to use their powers.
Gaia is desperate to face Little Pete, whom she calls Nemesis, in a battle to decide who will survive. She wants to kill Nemesis so she can leave the FAYZ and conquer the rest of the world. Pete, however, is beginning to fade from existence, since his sister, Astrid, tossed him to a horde of carnivorous insects. He saved himself by projecting his consciousness to some other realm, not in the FAYZ, but not in the real world either.
Pete learned that he can interact with others within the FAYZ, but when he does, he hurts them. His touch changes their DNA, morphing them into bizarre creatures, which often die. As Pete begins to weaken, Gaia is able to manipulate the dome, causing a thrill seeker climbing on it to fall through.
The man’s name is Alex. She rips off his arm for food, and then forces him to follow her so that she can continue to snack on him if she grows hungry. When she broke through the dome, it hurt Little Pete. One of the few lessons he remembers from being human is that it is not OK to hurt people. He realizes Gaia has been hurting people and resolves to find a way to stop her.
Sam heads down to Perdido Beach to enlist Caine’s help to kill Gaia. Edilio will take over the running of the town with the help of Quinn. Although reluctant at first, Caine agrees, mainly because of his unspoken love for Diana. Edilio asks Quinn to take a boat out to the island Alberto escaped to when he thought the FAYZ was going to stay in darkness. Without Alberto’s help to motivate the surviving children to harvest food, everyone will starve before the dome can come down.
Meanwhile, Brianna has found Drake, the sadistic minion of the gaiphage, who enjoys torturing others with his tentacle arm, using it as a whip to slash their bodies. Brianna uses her super speed, a thin wire and a machete to slice Drake into pieces. As he cannot be killed, the pieces try and reassemble themselves, but she takes them to different places, throwing some into the ocean, tossing others into the desert.
She takes Drake's head, which had been split into two pieces but then reattached itself with a lizard inside, and brings it to the lake community where she hopes to impress Sam with her trophy. As Sam has already left, Astrid takes charge of the monstrosity. She puts Drake’s head in a cooler, weighs it down with rocks, and sinks it to the bottom of the lake.
Lana, the healer, has been working to restore Taylor, a girl with teleportation powers. Little Pete had touched her, turning her into a misshapen creature with gold skin. Her legs and hands were amputated during the process.
Lana has tried to reattach them, unsuccessfully. Thinking that Taylor may be more plant matter than mammal now, she asks a girl with a green thumb to try splicing Taylor’s limbs back on. Eventually, Taylor regains enough of herself so she can teleport again. Little Pete reaches out to her and tries to undo some of the damage he accidently caused. She becomes more human, but still retains her golden skin. She is able to talk but will never be the same Taylor.
Albert agrees to return to Perdido Beach. He knows if he does not, and the dome comes down, he will be labeled a coward. By going back and motivating the children to work again, he will be a hero and will be able to write his own ticket to success when the dome comes down. He returns with Quinn and is able to get the children back to work, harvesting what little crops they have so they will not starve.
Diana learns that Gaia is intent on killing everyone within the FAYZ to prevent Little Pete from taking over a body and fighting her. Diana manages to escape and make her way to the lake community to try and warn them. Without Sam, the children have little hope against Gaia.
Gaia laughs as she slaughters many of the lake community. Brianna is able to shoot Gaia, severing the creature’s leg. The wounded Gaia limps off to heal.
She encounters Sam and Caine, who battle her together. Gaia cripples Sam’s body, breaking several of his limbs so he is unable to move. She is able to send intense pain into Caine’s brain, incapacitating him to the point that he is forced to follow her or be tortured.
The children of Perdido Beach try to ambush Gaia, but she is too powerful. Several are killed, including Brianna. Gaia escapes again to heal her wounds and finds Alex.
He has rescued Drake’s head from the lake. Gaia rips off Alex’s head so she can attach Drake’s head to Alex's body and restore her most powerful minion. Drake insists she restore his whip arm as well.
Drake begins to despise Gaia for her human weakness. His goal is no longer to serve her, but to find and torture Astrid and Diana. He captures Astrid and delights in whipping her. But Astrid has become stronger in the FAYZ and is able to bite off his nose and pop out one of his eyeballs. Before he can regenerate, she escapes.
The surviving leaders of the children have come to the realization that there are only two ways Gaia may be defeated. The first is to have Caine and Sam sacrifice themselves — by killing themselves or allowing Gaia to kill them. This will cause her to lose their powers. Without their strength, the nonmutant children would be able overcome her.
The second option is for another child to sacrifice himself or herself to Little Pete, allowing him to possess a body so he may physically fight Gaia. When missiles taken from an abandoned military base fail to kill her, three children — Astrid, Diana and Caine — call out to Little Pete and ask him to take over their bodies. In the end, Pete chooses to possess Caine in order to defeat Gaia. The two face off in an epic battle of light, burning each other into ash, until both die.
The dome over the FAYZ disappears and, with the sudden rush of oxygen, sets a wild fire that heads toward the beach. As kids flee to safety, Sam sets out to find Drake to punish him for hurting Astrid. Before they can fight, Drake’s regenerated body falls apart. The surviving children are taken to hospitals for treatment, and the dead are counted. A total of 332 had been confined in the FAYZ. About 136 died from starvation, accidents, flu, suicide, murder, coyotes and other animals.
Sam is kept separated from the other children in his hospital room. He has become the public’s scapegoat and calls to prosecute him fill the media. Caine, however, left two messages before he died. To Diana, he wrote that he loved her. But in another, left in the secluded island mansion of Hollywood royalty, he left a confessional note that everything that happened within the FAYZ was his fault.
Caine claimed he had the power to control people mentally, and he forced the others to do all the horrible things they did. The actors join with Astrid to write a book and screenplay about life in the FAYZ. Sam, Astrid and Diana get an apartment together in Los Angeles and attempt, along with the other survivors, to move on with their lives.