Since the suicide of his classmate a few years before, a young man named Tatsumi stays shut inside his parent’s house, refusing to leave his room and stuck in a limbo of confusion and grief. One day, something breaks inside him and he starts to run. He runs non-stop, as if something has awoken inside of him. His then finds himself wandering around the streets, searching for where to go. While searching, he comes across a strange funeral service, full of vagrants and drunkards. There he meets a vagrant named Tsuchiro and the two form a close bond.

In the 17th century, two Portuguese Jesuit priests travel to Japan in an attempt to locate their mentor, who is rumored to have committed apostasy, and to propagate Catholicism.

Hiro moves from Japan to New York with the dream of becoming a singer-songwriter. Once he meets the lovely Akiko, however, the lives and the lives of his friends Akira and Ken will never be the same.