Island unfolds on the remote island of Urashima, far from the mainland, where a man washes ashore with no memory of his name or homeland. The only thing he clearly remembers is that he is a time traveler on a mission to save a certain girl from harm. When night falls, he meets Rinne Ohara, a girl whose song brings the name "Setsuna" to mind, and he decides to take that name for himself.
Rinne, who knows another Setsuna, brings him into her household as a servant, hoping he may be the same person she remembers. From there, the man calling himself Setsuna is pulled deeper into Urashima's closed world, where local folklore, the three great families, and an endemic disease that keeps anyone afflicted from stepping into daylight shape everyday life.
As Setsuna searches for the truth behind his missing memories and Urashima itself, he must act quickly to complete the mission that led him there. Yet the more he witnesses the island's troubles and buried tensions, the more uncertain his purpose becomes, and he begins to wonder whether his displacement through time is really only an attempt to alter the fate of a single girl.