Children of the Whales unfolds in a world covered by an endless sea of sand, where a drifting island known as the Mud Whale carries a hidden town within its interior. Most of its inhabitants are said to be Marked, people whose supernatural abilities come at the cost of an untimely death. Chakuro is the village archivist; young and curious, he spends his time documenting the discovery of newfound islands. But each one is like the rest: abandoned save for the remnants of those who lived there long ago.
For the first time in six months, another island crosses the horizon, and Chakuro joins his friends in the scouting group that goes out to investigate. During the expedition, they find vestiges of an archaic civilization. Inside one of its crumbling remains, Chakuro discovers a girl who will change his destiny and the world inside the Mud Whale as he knows it. From that moment on, the story expands beyond the island itself, drawing him into a larger conflict between isolation, memory, and the fragile hope of contact with the outside world.