The novel's protagonist is a recluse who, convinced that the world will end soon, takes up residence in an abandoned mine and then attempts to sell tickets to his "ark" to people he deems worthy of saving from the apocalypse.

The novel begins with the protagonist, who calls himself Mole, going to a flea market in order to find people to live aboard his "ark," an abandoned mine that he has outfitted so that it will withstand the nuclear holocaust that he predicts is imminent.

After chasing the pair of them back to the ark, Mole and the insect dealer discover that the shills are not the only intruders: other unseen, unwelcome people have been prowling the dark corridors as well.

As a brigade of old men, a band of school girls, and a group of wayward youths all come to occupy the hull of the "ark," Mole is forced to abandon his creation, his sanctum breached and his heart broken by the female sakura who rejects his advances.

In his review of the novel for The New York Times, Edmund White described The Ark Sakura as dreamlike "in the strictest sense,"[1] praising its scope and the level of detail of the novel.