The story focuses on a boy called Chakuro, who lives on a giant vessel called a Mud Whale that drifts over the sea of sand. In the Mud Whale, society is divided into two kinds of people: the Marked, who can move objects with their minds using a strange power called "thymia", at the expense of shortened lifespans, and the Unmarked, people who lack thymia but enjoy longer lifespans. Chakuro and his friends have never seen anyone from the outside world, and they spend their days yearning to explore and learn about it. In year 93 of the vessel's exile, the Mud Whale encounters a lonely island and Chakuro finds a girl inside, starting an adventure that changes the lives of everyone.