In times of need, if you look in the right place, you just may see a strange telephone number scrawled in red. If you call this number, you will hear a young man introduce himself as the Yato God. Yato is a minor deity and a self-proclaimed "Delivery God," who dreams of having millions of worshippers. Without a single shrine dedicated to his name, however, his goals are far from being realized. He spends his days doing odd jobs for five yen apiece, until his weapon partner becomes fed up with her useless master and deserts him.

1989年，日本。
乔纳森·乔斯达与DIO决战后的一百年，DIO复活了。同时，乔瑟夫的孙子，空条承太郎发现自己有幽波纹（替身）能力，DIO的复活影响了没有替身抵抗能力的母亲，陷入病危情况；为了拯救命在旦夕的母亲，承太郎与乔瑟夫出发前往DIO的所在地——埃及。