The following version of this book was used to create the guide: Starmer, Aaron. The Only Ones. Delacorte Press, 2011.

The novel begins by introducing Martin Maple, a nine-year-old boy, and his father, who live in a cabin on an island with very few inhabitants. Martin forms a connection with a boy named George, who comes over every summer for vacation. Meanwhile, Martin's father works on a mysterious machine whose purpose Martin does not know. One day, he goes out to town to get a piece for the machine, and never returns; nor does George. After a year of solitude, Martin sets out on a boat toward where George usually would come from.

He lands in an abandoned town and is chased out of the library by a bear. Then, he meets a boy named Kelvin, who tells him about something called the Day where everyone left. He tells Martin to go find Xibalba, a society where the few survivors, all children, have banded together. He eventually finds them, and they label Martin a Forgotten. Darla, a leader of sorts, introduces Martin to everyone and tells him this is everyone left in the world.

Martin sets up solar panels for everyone in the village. He learns that Kelvin founded Xibalba, but was banished. Darla shows up and takes a marble out of Kelvin's "Internet" page (the Internet is a series of physical tablets with info written on them). Martin learns how all the children found Xibalba, and he hides a book his father gave him and an address for where his father used to live in his own Internet page. Felix, the creator of the Internet, introduces Martin to Lane, a mysterious girl, and then Nigel, another enigmatic figure, summons Martin to his house.

Nigel, who can predict the future, tells Martin that the machine his father was building is the key to bringing everyone who disappeared back. He gathers a few of the children to build the machine again. They set up shop at an abandoned theme park, and Martin tells them this is the key to bringing everyone back even though he does not know how to complete the machine physically. One night, an accident at the theme park kills a boy named Chet, despite Lane and Martin's attempts to save him. They arrive back and evade the other children's questions about why they were there. Then, Darla is summoned to Nigel's house, and after, she says she knows what the spaceship needs to be complete. She tells Martin the marble she took from Kelvin's page is what is needed, and tells him he needs to do things for her in order for her to give it to him. They transport the machine back to town.

Darla tells Martin he needs to go on a date with her to get the marble. They go bowling together and see a movie, and Darla gives him the marble. They leave the theater and see Felix being chased by Nigel's Komodo dragon; the truck he drives spits out flames, which kills the lizard but sets Nigel's house on fire. A tiger chases him back to his house and he shoots it there. His house is also set on fire, and Martin and Darla go over to find Henry trying to steal the book Martin's father gave him. Darla kills the tiger, and then Nigel comes over and, furious that his tiger was killed, kills Felix.

The fire rages through town the whole night. After it goes out, Henry is banished to six months in the Ring of Penance outside of town. Martin lies to the kids and says that Nigel told him before he disappeared that everyone should trust him. Later, Lane tells Martin that Kelvin was banished because he led an expedition underground to find the missing people, but many people were killed due to a mine shaft collapse. Meanwhile, everyone helps Martin with the machine. When it is finished, the marble does nothing, and Martin is afraid. Everyone gets into the machine, and something happens, but they step outside and find themselves still in Xibalba and not transported somewhere like they expected. Everyone turns on Martin, and Darla suggests Martin hide out somewhere.

Martin stays in the abandoned hospital for awhile until he meets a woman named Marjorie there unexpectedly. She tries to kill Martin until Henry saves him. When Martin comes to, he follows where the woman walked and coaxes her to come out and talk to them. They knock her out and take her back to town. Martin surmises that Marjorie is Kelvin's mother, and Martin believes that the machine brought her to them. Henry puts a gift from his father where the marble went in the machine, and it brings his father back. His father is angry and says that he is taking Henry away.

On the night before Henry leaves, they hold a big dinner. A boy named Trent leaves the dinner to go summon his mother. After everyone eats, Martin gets sick; people call him back, though, and he returns to find everyone has been poisoned except for Henry. Henry and his father have poisoned the food with mushrooms so they can steal the machine and leave. Martin passes out after attempting to stop him, but he wakes up later to see Trent's mother, a doctor, taking care of him. He was in a coma for three months, but almost everyone has been saved from the poison with a few exceptions and Henry and his father fled. He learns that Trent has been bringing back many people every day. Then, Martin brings Kelvin back.

In the ensuing days, Martin brings many people back himself, as everyone leaves the society. He summons George back, and he leaves with his family. One day, George returns saying he visited the address of Martin's father and brings back a note from Martin's mother. Martin summons her successfully and promises her they will find his father.