It is the year 2046, Noboru Terao and Mikako Nagamine are close friends who will soon be graduating junior high school. But after an alien attack on humanity, Mikako is selected for the UN military space expedition set to retaliate against the aliens. Separated, Noboru and Mikako attempt to keep in touch by sending emails to each other with their cell phones. Yet as the expedition journeys farther from Earth, the time it takes for them to transmit and receive each other's messages increases substantially.

Hoshi no Koe revolves around the relationship between this couple as they try to stay connected despite the growing distance between them.