Yomi no Tsugai is set in an isolated village where twins are born under a strange division of day and night, and where Yuru grows up as a hunter of animals while his sister Asa is kept in a cage and assigned a special duty that limits who can meet her.
That fragile balance shatters when armed men riding helicopters, called "dragons" by the villagers, storm the village in search of Yuru and kill every adult on sight. As Yuru tries to reach Asa and escape, he is drawn into a deeper crisis, with the aftermath of the assault and a mysterious woman tied to the attack claiming to be his true twin sister.
Yuru is rescued by Ryuu "Dera" Tadera, an outsider who frequently visits the village, but their relief is short-lived and the two are soon cornered again. In a desperate attempt to survive, Dera forces Yuru to offer a gift to the village deity, summoning a pair of daemons whose existence begins to expose the truth behind the raid, the twins, and the hidden power binding the village together.