Unable to sleep at night, Ganta Nakami is cranky in class and unpopular with his classmates. He discovers that the school observatory, once used by the now-defunct astronomy club, may be the perfect place for a nap--but he's not alone. Fellow insomniac Isaki Magari is willing to share the observatory with Nakami, and a friendship between the two begins as they bond over the most unlikely things.

Ganta and Isaki are on their astronomy club's summer trip, but when Isaki's older sister (and their chaperone!) ditches them, they're left all alone. Free from their daily obligations and lost in the bliss of summer, they feel time seeming to slow down. After the trip takes a surprising turn, they reach their final destination: the starry sky of the Mawaki ruins.