Gone.

Every person at the age of 15 or over vanishes from the town of Perdido Beach and causes great confusion and chaos. Some are happy, some are anxious. Sam Temple, Astrid Ellison and Quinn Gaither set out to explore the area, discovering a barrier cutting the area off from the outside world with a radius centered at a nuclear power plant located outside of town. The area within the barrier is nicknamed the Fallout Alley Youth Zone or FAYZ for short. Exploring this nuclear power plant, the group finds Astrid's severely autistic 5-year-old brother Pete, along with a map marking radiation patterns from a 15-year-old explosion at the plant that lines up exactly with the energy barrier. Sam and Pete are revealed to have supernatural powers caused by the power plants explosion 15 years ago. Upon the group's return to Perdido Beach, its members encounter vehicles bringing students from nearby Coates Academy. Some of the students and others in town have supernatural powers, including Lana Arwen Lazar (who has the powers which she discovered after she and her dog, Patrick, were wounded after her Grandfather vanished causing his truck to crash and they were attacked by a coyote pack that abducted her earlier.) Caine Soren, a boy who also has supernatural powers, takes a group and returns to Coates Academy, discovering that when a person turns 15, they are confronted by something they desire before vanishing. He also discovers that he and Sam are twin brothers. Sam's group (Astrid, Quinn, Pete and Edilio Escobar, a boy who was in their class) finds Lana and he and the group escape the coyotes but are captured by Drake and imprisoned within Coates Academy. Sam's group escapes Coates Academy, joined by various Coates students, and returns to Perdido Beach to fight Caine. Meanwhile, Drake abducts Lana as he thinks she can help him get his arm back after Sam had burned it off. They reach a creature known as the "Darkness" down a mineshaft which uses Lana's power to give Drake a whip for an arm giving him the nickname "whip hand". Caine attacks the town with the help of the coyotes, and Sam and Caine fight in the town square. The two turn 15 and encounter what seems to be their mother, but Caine understands what is happening and refuses to go with her. Sam follow suits and neither "poof", making Sam the oldest in the FAYZ and Caine second. Caine and his group returned to Coates Academy while Sam becomes the leader of Perdido Beach.

Hunger.

Hunger is set three months after Gone. Fueled by a widespread prejudice against people with powers, Zil creates the "Human Crew", an organisation that discriminates against these "freaks". E.Z. dies when he goes to the fields as new creatures, called Zekes, have mutated and attacked him. 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.

Lies.

A young girl named Jill is beaten due to some people's knowledge of her powers and falls into an empty grave. Sam discovers her and is told by Edilio that she was in the grave of a girl called Brittney, who has been dead for a month but seems to have disappeared. Astrid and Sam find a boy attacked by Drake, who has been seen nearby. Sam learns that Brittney is alive and in town, and meets an unfamiliar girl named Nerezza. Nerezza eventually attempts to kill Pete, who is revealed to have created the energy barrier, but fails when Astrid intervenes. When Pete finds his favorite toy smashed on the ground, he screams, causing the energy barrier surrounding the area to disappear for a brief moment. Astrid sees adults staring on the other side before the wall returns. The gaiaphage is revealed to have been attempting to use Brittney's immortality and Lana's healing powers to bring Drake back from the dead but sharing the same body as Brittney. Nerezza is not human at all, but rather the gaiaphage's avatar, brought to life through Pete's thoughts. After fighting Drake long enough for him to turn into Brittney, Sam decides not to kill the two but rather have them locked up guarded by Orc, a boy made out of gravel, as he experiences no pain at being whipped by Drake.

Plague.

Perdido Beach is now run by a boy named Albert Hillsborough, whose introduction of capitalist systems to the town has placed him in a position of considerable power. Albert sends Sam and others on a mission to find a new water source, Lake Tramonto, on the far side of the FAYZ, as the town's supplies are running low. Meanwhile, an infectious plague leading those who catch it to almost certain death is spreading in Perdido Beach. On the way to the lake, Sam's group encounters an old friend named Hunter who was banished from the FAYZ with the power to radiate heat within anything who has become infested with parasites and dies. A coyote who leads them to creatures that are causing parasitic insect infections. The group attacks the creatures, but Dekka becomes infested with insects in the process. Sam later saved her by cutting her open and removing the parasites. Upon reaching the lake, the group is once again confronted by the creatures, which have grown to the size of SUVs and are being commanded by Drake. The group escapes back to Perdido Beach. Drake travels to Coates Academy with some of the insects, having been commanded by the Gaiaphage to capture Pete. Upon their arrival, Astrid throws Pete to the insects, who realizes the danger and vanishes both the insects and himself; her hope was that Pete's death would cause the energy barrier to dissipate. Pete is later revealed to be bodiless but alive.

Fear. 

Pete experiments with his new state of existence by tampering with the inhabitants of the FAYZ, resulting in gruesome deaths as he clumsily changes their DNA. The energy barrier begins to turn black, gradually filling the Zone with darkness. On the outside of the barrier, Connie Temple (Sam and Caine's mother) learns that a small part of the army plans to nuke the barrier. Through mental communication with Pete, Astrid learns that the barrier is connected to the gaiaphage. Drake captures the pregnant Diana and brings her to the mine shaft. Diana gives birth to her baby, whom the gaiaphage then inhabits. Drake, Diana, Penny and the gaiaphage, now known as Gaia, head to the energy barrier, where they encounter Sam and Caine. The gaiaphage plans to open up the barrier. They battle, and Sam attacks Gaia; sunlight instantly returns to the FAYZ as the energy barrier becomes transparent. Sam once again attacks Gaia, who is seemingly unhurt. She flees the scene along with Diana and Drake. Visual communication begins between the inhabitants of the Zone and the outside world.

Light. 

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Light is the final book in the series. The dome around the FAYZ has become transparent, allowing the kids inside to converse with their parents. Some, such as Brianna, are thrilled to have the attention, while others, like Orc, are ashamed of what they have become and pray that the dome never comes down. In the thrill of being able to converse with the outer world, the kids lose interest in their duties, which leads to sending Quinn to the island to get Albert, as he is the only one who can get them back to work. Annoyed at Brianna, Sam and Astrid send her on a mission to hunt for Drake. She succeeds, and scatters the chopped off parts of his body across the landscape, keeping his head in a chest below the boats on the lake.
Meanwhile, Gaia and Diana are out in the desert, where a rapidly aging Gaia schemes to take out all of the FAYZ residents in order to put an end to Little Pete's powers, who gets his strength through the power of the other FAYZ residents as she does. Intending to stop Gaia and rescue Diana, Sam and Caine go on a hunt for Gaia together. However, when they find her later, she easily defeats them, but leaves them alive. Gaia proceeds to attack the lake, and with few powers to protect it, the kids there are slaughtered and several minor characters are killed. The kids regroup at the town and discuss what to do next.
It is revealed that Gaia, though possessing every power of every living person in the FAYZ, loses that power when the person dies. Sam contemplates whether he must sacrifice himself in order to stop Gaia. Meanwhile, after saving Drake by connecting his living head to the body of a man she killed, Gaia attacks the town and kills Brianna. Computer Jack is killed by a stray bullet during the battle. With the situation desperate, Caine goes to get Albert's missiles and launches them at Gaia. They hit the FAYZ wall and kill Orc, who was fighting Gaia at the time. Realizing that there is only one option left, Caine invites the spirit of Little Pete to take control of his body, and using it Little Pete fights Gaia, sacrificing both himself and Caine but killing the gaiaphage as well.
After the FAYZ wall comes down, Sam has a final encounter with Drake and defeats him. The remaining kids reunite with their parents and mourn their losses. To get them out of legal trouble, Caine had written a confession note prior to his death claiming that he was controlling the kids and making them do all of the things that they did. The series concludes with Sam and Astrid inviting Diana to come live with them, to which she agrees.