A few days after the events of Fear, Gaia and Diana survive out in the deserts of the FAYZ, living off scraps of food that Drake, under orders, scavenges for them. Gaia is undergoing a steady healing process after the attack from Sam Temple and Caine left her incredibly wounded.
Meanwhile, Sam and Astrid are attempting to maintain order at Lake Tramonto after the now transparent FAYZ Wall attracts the kids of the FAYZ in hopes of reuniting with their parents. Food production grinds to a halt, and in Perdido Beach, Caine begins to lose control of a workforce that refuse to do anything except gawk at the outside world. The Media attempt to interview the FAYZ residents through electronic signs and communication; an interview with Brianna reveals the true nature of life inside the FAYZ and the world outside begins to realize the true horrors within. Irritated at Brianna's reckless behavior, Sam and Astrid send her out patrolling to keep her out of trouble.Edilio, in an attempt to strike first, asks Sam to travel to Perdido Beach with him in order to attempt a truce with Caine. Caine, bored and frustrated, refuses until Edilio and Sam subdue him long enough to convince him to help. Leaving Edilio in charge of Perdido Beach, Caine and Sam head off into the wilderness in hope to find and kill Gaia, and, in Caine's case, rescue Diana.
Out in the desert, Brianna runs into Drake, and using her Bowie Knife, catches him unaware and slices him into many pieces. Taunting him, she spreads his body parts around the FAYZ, locking them in cars and throwing them into the ocean. Victorious, she takes his severed head to Lake Tramanto to show Astrid and Dekka - who lock the head away in a container, weigh it down with rocks, and throw it into the lake.
With the absence of Drake, Gaia grows ever more hungry. It is revealed that all trace of the once human child Gaia, now inhabited by the Gaiaphage, is utterly destroyed - though the body itself is in constant danger and can be killed through a united effort. Gaia tells Diana that she holds a connection to the strange, cororpeal world that the mutations and powers of the FAYZ exist in. In essence - Gaia has access to ALL powers, Light, Speed, Telekinesis, Healing, etc. She reveals that the powers exist as a two-way connection - by killing a mutant, she cuts off access to that power and can thus no longer use it herself. Unfortunately, Little Pete is too powerful for her to directly control, and she states that in order to prevent him from taking a body to stop her, she must kill the entire population of the FAYZ in order to destroy him and bring down the wall.
Later, Diana and Gaia stop near a part of town. Outside that area, a man (who is later revealed to be a man named Alex Mayle) attempts to climb part of the wall using a ladder. Still hungry, Gaia mentally "hits" little Pete in order to weaken the barrier long enough for the man to fall through the barrier. He is attacked by Gaia, who rips off his arm, then cooks it so she can eat. Little Pete grows angry at this act, for, as he puts it, "it is not okay to hit". Worried, Gaia hastens to Lake Tramonto in order to begin her massacre.
On the outside, Nurse Connie Temple attempts to contact Astrid or Edilio in order to prepare the kids inside for the behaviour of the outside world. Protests and polls spring up against trying to break down the wall, prosecuting the children inside and killing the inhabitants with a bigger nuclear bomb than that used in Fear. A video of Gaia eating Alex's arm is released onto the internet, and public opinion radically shifts. Unable to contact anyone, Dahra Baidoo offers to take Connie's message to Astrid, and travels to Lake Tramonto. She is attacked by Coyotes on route and saved by Orc, who carries her the rest of the way. Back in Perdido Beach, Edilio asks Quinn to retrieve Albert from the Island. At some persuading, Albert returns and forces the parents and media to stay away from the barrier, leaving blunt signs that outlay the consequences: stay and watch and the kids will die, or leave and let them work.
Under cover of night, Gaia reaches the lake and begins a mass slaughter on the uprepared and defenseless residents using Sam's power of light, including Dahra, who dies in an explosion, and Justin, Roger's friend. Many die defenseless until Brianna manages to subdue Gaia, though she is terribly wounded in doing so. Gaia, unable to kill Brianna for fear of losing the speed power, retreats, bleeding and shocked that she could be defeated. The wounded load onto the lake's only working car and head for Clifftop Hotel, whilst the remaining survivors head on foot to Perdido Beach. Sam and Caine follow the smoke to Gaia, who defeats them easily, using her mental "hooks" in Caine to send him into a madness. She starts a fire in order to force the FAYZ residents into Perdido Beach to make it easier for them to kill. Sam and Caine give chase again, and in anger, Gaia breaks Sam's spine and forces Caine to be her prisoner, threatening him with the intense mind pain she can cause in those who have been in prior contact with her.
At Clifftop, Lana and Sanjit manage to heal Taylor with the help of Sinder's power of with plants. Taylor regains her mind and bounces away, whilst the wounded of Lake Tramonto, including Diana, who escaped, beg for Lana's aid. Little Pete reaches out to Taylor and partially heals her golden skin condition, apologized for changing her and asking for her help to fight the Gaiaphage. Diana reveals what she knows of her daughter to Astrid, Lana and Edilio. A town meeting is called and come to realization the FAYZ resident's have two options: convince Little Pete to take a living human sacrifice to kill Gaia, or kill Sam and Caine in order to cut off Gaia's most dangerous weapons in hopes of defeating her. Astrid and Diana both silently beg for Little Pete to take them in order to spare Sam and Caine's life.
Lana begs for Edilio to attack the Gaiaphage whilst it is recovering, and Edilio sets up an ambush. Gaia walks into Dekka's gravity trap, though using her combined powers she nearly kills Dekka. Brianna, rushing out to help before she is fully healed, almost single-handedly kills the Gaiaphage, though her inability to go faster than Gaia and her injuries allow Gaia to defeat Brianna and use Sam's light to burn out her heart. No longer having access to the power of speed, Gaia retreats, leaving Dekka and Edilio to grieve over Brianna's body.
Back at the lake, Connie Temple and the media see the debris of the massacre and begin to lose hope. Alex Mayle, having been left behind at the lake, find's Drake's head in the water and is convinced to bring it to Gaia, who severs Alex's head and reattaches Drake's also providing him with a new and more powerful arm. Drake convinces Gaia to let him find Astrid, who allows him too under the hope of having a hostage personal to Little Pete.
Taylor finds a mangled and broken Sam on the highway and at his request, gets Quinn to take him to Lana. Lana heals him, though the process is slow, and Astrid updates Sam on what is happening. Horrified at how Gaia is using his power of Light and at Brianna's death, Sam walks out alone to face Gaia, knowing that if he cannot defeat her, he will sacrifice himself to prevent her from using his power. Gaia defeats him easily and binds him in burning chains after Sam tries (unsuccessfully) to kill himself. Victorious, Gaia marches on Perdidio Beach, using telekinesis dragging an imprisoned Sam behind her.
In order to fight her. Caine reveals that he has asked Little Pete to take him if the plan goes sour, and pushes Diana away in a boat in order to keep her away from the fight. Meanwhile, with Sam gone, Drake captures Astrid and begins to whip her with his arm. Astrid begs silently for Sam, and stalls Drake long enough to get close to him and bite down on his nose. After enough force, she bites his nose clean off before Taylor appears, sent by Little Pete to help her.
With Sam injured and Caine missing, Gaia begins an easy slaughter on Perdido Beach. Edilio and the remaining powers fight a last stand against her and Jack, who at first was unwilling to fight, steps up long enough to save Sam from his chains but is killed by a stray bullet. Losing Jack's power of strength, Gaia flees into the church where she is greeted by Dekka, who narrowly loses the fight. Gaia heads for the FAYZ barrier where many kids have escaped the massacre. Her beams of light manage to cut through the weakened barrier due to Little Pete's "fading" state, killing adults on the outside as the helpless world watches on.
Orc, who had stayed away from the barrier for fear of being seen, manages to save the remaining children long enough for Caine to arrive. Gaia is shielded by Caine's missile from Orc's body, which is blasted apart. Left with no other option, Caine asks Little Pete to take over his body. It is revealed that the Gaiaphage itself created the mutations by its very presence, and Little Pete, most vulnerable due to his damaged state, became the Gaiaphage's own created nemesis. Not knowing what he was doing during the meltdown, Little Pete created the barrier as a method of protection against the noise, the grown-ups and, unknowingly, the Gaiaphage itself.
With the world as witness, Gaia and Little Pete open fire on each other. The two disintegrate, and with the ultimate death of Little Pete and the Gaiaphage, the FAYZ wall comes down. The residents of the FAYZ flee from the oncoming fire, though Sam, noticing Astrid's whip wounds, runs back to confront Drake. In an effort to burn him with his light, Sam finds he cannot use his power due to the death of the Gaiaphage. Coming to this realization, Drake's transplanted head falls from his body and Sam tosses it into the flames before leaving the FAYZ forever.
During the last two chapter of the book, the aftermath is revealed. In his letter Caine takes all credit for actions in the FAYZ hence wiping all the kids' records. When it turns out Roger was really alive Edilio asks his parents to meet him. Sam confronts his mother finding out that his dad 'created' the Gaiaphage. In the end Astrid and Sam invite Diana to live with them.
- Alex Mayle - Decapitated by Gaia
- Brianna - Heart burned by Gaia
- Caine - Sacrificed his body to Little Pete
- Orc - Accidentally blown up by a missile by Caine fired at Gaia
- Dahra Baidoo - Killed in an explosion by Gaia in the Lake Tramonto attack
- Drake Merwin and Brittney Donegal - Burned by Sam
- Gaia/Gaiaphage - Burned by Little Pete
- Jezzie - Killed by Gaia in the Lake Tramonto attack
- Justin - Burned by Gaia in the Lake Tramonto attack
- Computer Jack - Accidentally shot
- Little Pete - Burned by Gaia
- Spartacus - Burned by Gaia