The same basic storyline is followed by the manga and anime, with a few small changes between the versions. While exploring his grandfather's shed, Hikaru stumbles across a Go board haunted by the spirit of Fujiwara no Sai, a fictional Go player from the Heian era. Sai wishes to play Go again, having not been able to since the late Edo period, when he possessed the body of Honinbou Shuusaku, an actual Go player of that period. Sai's greatest desire is to attain the "Kami no Itte" – "Divine Move," or the "Hand of God" – a perfect game. Because Hikaru is apparently the only person who can perceive him, Sai inhabits a part of Hikaru's mind as a separate personality, coexisting, although not always comfortably, with the child.

Urged by Sai, Hikaru begins playing Go despite a lack of interest in the game. He begins by mimicking the moves Sai dictates to him, but Sai tells him to try to understand each move. In a Go salon, Hikaru defeats Akira Touya, a boy his age who plays Go at professional level. Akira subsequently begins a quest to discover the source of Hikaru's strength, an obsession which will come to dominate his life.

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