An island known as the Mud Whale sails in a planet blanketed by an infinite sea of sand. In its interior is an old village, the bulk of whose people are supposed to be "Marked," a dual-edged feature that provides them extraordinary talents at the cost of an untimely death. Chakuro is the village archivist; youthful and inquisitive, he spends his time chronicling the discovery of newly discovered islands. But each one, like the others, has been abandoned, save for the relics of people who formerly lived there. Another island appears on the horizon for the first time in six months, so Chakuro and his buddies join the reconnaissance group. During the journey, they discover relics of an ancient civilisation. And inside one of its collapsing buildings remains, Chakuro discovers a girl who will change his destiny and the world inside the Mud Whale as he knows it.