Nathan, a sixth grader in New York City, spends a locked-in morning re-reading
Calvin and Hobbes comics. His parents have confiscated his devices, and his door is locked from outside. Nathan eats every item of lunch because his mother records his calorie intake in a daily logbook. Earlier, his mother told him there would be no school: They are going to the Wagon, the spaceship where their community lives, because Hester, their leader, wants to see him. His cat, Toto, who understands human speech, paces the kitchen like a guard.
Nathan has kept an enormous secret his entire life. He believes he is Kast, a member of an alien species from a distant planet, and his sole purpose is to remain undetectable among humans. On the family's first vacation in Florida, he discovered a bump on his lower back that his father identified as a tail. His parents reported the development, triggering Hester's summons. Nathan sends a cryptic goodbye to his best friend, Victor, and writes him a letter explaining that the Wagon is a spaceship where his parents grew up during an 18-year journey from Kast.
Victor shows up uninvited and Nathan reveals the truth. Victor asks to see the tail, which has grown since Florida: about two hands long, orange with a black tip, and moving on its own. Two men then arrive whom Nathan nicknames Sad Shoes and Egg-lover. They are Wagon messengers sent to collect Nathan alone, but his mother calls Hester and secures permission for the whole family to go. The family departs by train to Altoona, Pennsylvania, while Victor watches helplessly from behind a mailbox.
Through flashbacks, the story establishes Nathan's bond with Isabel, a Kast girl in Illinois he calls Izzy. They met at an Ohio rest stop where their families exchanged special pink toothpaste used to maintain human appearance. Izzy pressed a bracelet and phone number into Nathan's palm, and they texted every night. Their conversations reveal exhausting Kast rituals: daily toothpaste use, calorie counts, and the logbook Nathan's mother fills out about him. Over the past year, several Kast children have disappeared from virtual meetings without explanation, and Izzy was the most recent.
The Wagon is disguised as a massive blue storage center behind a mall in Altoona. Inside, approximately 20 Kast adults clap for Nathan, led by Hester, a young-looking white woman whose apparent youth puzzles him. At a meager banquet, Nathan refuses to eat until Izzy is brought to him. She arrives exhausted, in a faded jumpsuit with cracked lips. Before being dismissed, she drops a torn napkin printed with a tiny "6." That night, Nathan's mother reveals Section Six is the worst work assignment on the Wagon. Nathan also realizes his mother's logbook is only about him: He is her experiment.
Nathan navigates the Wagon's mossy hallways to Section Six. The locked door opens in response to his tail's wiggling. Inside, he finds Leo from Louisiana, another recalled Kast child he knows from the monthly virtual meetings, and Izzy. Izzy did not change when she turned 12: She failed the experiment by remaining fully human. None of the recalled children changed. She presents a radical theory: They may not be aliens but humans whom Hester is transforming using the pink toothpaste. Nathan's tail, which she insists he name Tuck, would be Hester's first success, a Kast entity bonded to a human body. Izzy reveals she and Leo are now dating and that her parents have been reassigned as Decommissioned Parents—former experimenters stripped of their roles and put to work maintaining the Wagon. Nathan races back to tell his parents. His father rejects the theory; his mother is cautious. Hester sends the family home.
Back in New York, Nathan reconnects with Victor and introduces him to Tuck, who taps Victor's hand in greeting. Nathan's parents argue; his mother notes the Wagon has no windows and questions whether they were ever in space. One night, Tuck spells "HLP" with pencils on Nathan's floor, a plea for help that his parents dismiss. Toto leads Nathan to a forgotten shoebox in his parents' closet. Among old devices from the Wagon, Tuck activates an egg-shaped object that flashes pink, shows green moss, then goes dark. Nathan decides to return to the Wagon. His mother watches through a hidden camera and chooses not to stop him, having stolen the egg from the Wagon years ago to ensure the ship could never leave without her.
Nathan and Victor take the train to Altoona, but the retinal-scan gate does not recognize Nathan. At the mall, he encounters Egg-lover, whose real name is Martin. Martin agrees to drive Nathan through, and Nathan leaves Victor behind. Inside, he reunites with Izzy, Leo, and Annie, Martin's daughter. Izzy shares information learned from Miriam, another recalled child who fell from her platform and has not been seen since. A detachable engine called the Middle waits in space to retrieve the Wagon, but Hester prevents this by having workers scrub Kast moss off the bars spanning the open top. Nathan and Leo find Hester's quarters, where dated journals prove the Wagon was never in space during his parents' childhood.
Nathan discovers Hester's laboratory and a pool of opaque pink liquid. After falling in, he finds Hester suspended underwater. On the lab floor, Hester reveals the full truth: The Kast are not humanoid aliens but microscopic pink spores she discovered as a child. Hester is fully human, over two centuries old, kept young by the spore pool. She found the Wagon, a genuine Kast spaceship disguised as a mossy hill, and raised 40 human orphans aboard it, training them to believe they were alien explorers on a windowless ship. The toothpaste and other products contain spores designed to bond alien organisms to human hosts. Nathan's parents' entire identity was Hester's invention. He tricks Hester into leaving, finds a door-release button, and escapes with three journals.
The children become anti-scrubbers, tying harvested moss to the bars atop Section Six. That night, a vibration shakes the Wagon, and the Middle appears overhead. Everyone evacuates, but Nathan hears Victor's voice calling from deep inside the ship and turns back. In Section Six, the door locks behind him and the voice falls silent; Tuck mimicked it to lure Nathan back. The egg in his pocket chirps at the Middle. Nathan holds it out to Tuck, declaring his trust. Tuck taps the egg silent, but the Middle descends onto the Wagon anyway. The walls rise; Nathan realizes Section Six was never part of the ship but an open cylinder at its center. The Wagon lifts away, leaving him on bare ground. Tuck separates from his body as a wispy pink cloud and rejoins the Kast. Victor appears, truly present this time. Neither notices three spores drifting down to Nathan's bracelet.
An epilogue reveals Hester was nine in 1734 when she discovered the spores after falling from her horse, Castor, for whom she named the Kast. Aboard the departing ship, a calico cat settles in her lap and her heart begins to open. Three spores chose to remain on Nathan's bracelet, still calling themselves Tuck. In a final chapter, Nathan's life has settled: Annie and her father live in Victor's building, Nathan's mother attends college, and Nathan remains close friends with Izzy. He keeps the inert egg on his desk and gave Hester's journals to his parents. The book closes with Nathan knocking on his parents' door using the same words his father always used to wake him, now reversed, signaling a family rebuilt on honesty.