Chapters alternate from Ky’s and Cassia’s perspectives. Crossed begins with Cassia in a work camp for Aberrations, people who are not allowed to marry because they or their families have committed infractions against the government.
There, Cassia meets Indie, another teen girl. When a group of girls, including Indie, leaves the camp on an air ship, Cassia goes with them so she can reach a village in the Outer Provinces. She hopes to find Ky there, the boy she believes is her perfect match.
The Society, the name for the reigning government, routinely imports children into the outer villages to replace those killed by the Enemy. The Society wants the Enemy to believe these villages are occupied by a thriving farming community. Every night, the Enemy’s air ship fires on the village so there are few survivors. The occupants come to believe that the Society uses the Enemy’s fire to kill off Aberrations. After arriving in the village, Cassia and Indie learn that Ky had been there but had escaped. A boy leads them into an area of canyons and caves called the Carving so they can escape the village and search for Ky.
Ky is intent on returning to the Society to search for Cassia. He escaped the village with two others, Vick and Eli. They find their way into the Carving. Ky, Vick and Eli find an abandoned village that belonged to Anomalies.
They climb to the caves where they find provisions, books and maps collected by Anomalies or farmers, returning to the Carving to shelter for the night. The next morning, Ky awakens to the loud noise of something bombing the nearby river. Eli tells him that Vick had gone out fishing. When the noise stops, they investigate and discover that the Society has bombed the river with spheres of poison. They find Vick dead. After burying Vick, they are about to return to their camp in the Carving when Eli spots Cassia and Indie in the distance.
The teens return to the Carving together. They decide to return to the village. At the village, they see a farmer burying his daughter, and meet a young man named Hunter. Hunter is the sole survivor of the township. They agree to help each other. Hunter says he will help them find the Rising, a group that is rebelling against the Society. In exchange, he wants to take them to the Cavern in the Carving and have them explain what’s inside.
The Cavern is filled with thousands of tubes containing human tissue samples. The Society wants to keep these samples so they can recreate each person, if need be. Hunter reacts by smashing the tubes, which sends an alarm to the Society.
The teens flee the Cavern, except for Hunter, who remains a short time longer to continue smashing tubes. They return to one of the caves to gather papers. Since there are only a set list of books people are allowed to read, Archivists will pay or trade well for pages not on the set list. They hope the pages will help them get information that will lead them to the Rising.
Hunter finds a boat that seats only two, but it will help those two reach the Rising quicker. The others have to travel on foot. When Eli chooses to go to the mountains with Hunter to search for other Anomalies and Ky volunteers to go alone on foot, Cassia and Indie travel using the boat.
Members of the Rising find Cassia and Indie on the river, tow them in and interview them to determine how they can best be used. They want Cassia to return to the Society. When Ky arrives, they want him to be an air-ship pilot. Indie’s assignment is undetermined. Crossed ends with Cassia situated in Central, trading with Archivists and about to meet an unnamed person.