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 Hon'inbo Shusaku, 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 Toya, 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.
Hikaru becomes intrigued by the great dedication of Akira and Sai to the game and decides to start playing solely on his own. He is a complete novice at first, but has some unique abilities to his advantage; for instance, once he has a basic understanding of Go, he can reconstruct a game play by play from memory. Through training at Go clubs, study groups, and practice games with Sai, he manages to become an insei and later a pro, meeting various dedicated Go players of different ages and styles along the way. While Hikaru is at this point not yet up to the level of Akira, he demonstrates a natural talent for the game and remains determined to prove his own abilities to Akira, Sai, and himself.
Sai still passionately desires to play Go himself. During one summer break, Hikaru lets Sai play Go with other players on the Internet. The brilliant play of the mysterious user "Sai" soon becomes a worldwide sensation. However, Hikaru and Sai are forced to give up Internet play when Akira begins to suspect that Hikaru may be "Sai". Much later, Hikaru meets one of the boys he played online, who upon seeing his style of play correctly identifies him as a student of Sai's (thinking, of course, that Sai is a living person). Later on, Sai returns to the Internet to challenge Akira's father Toya Meijin, as it is the only way he can play the Meijin without arousing suspicion. Sai wins, but Hikaru notices that if the Meijin had played one move differently, he would have won instead. Witnessing Hikaru's personal growth, Sai realizes that the reason he was allowed to meet Hikaru was not to achieve the Hand of God, but for Hikaru to watch the match between Sai and the Meijin, and in a larger sense, to introduce Hikaru to Go.
Several days afterwards, Sai vanishes while playing a game with Hikaru. A distraught Hikaru searches for him, traveling to Shusaku's grave and collections of his relics. When these searches prove fruitless, Hikaru concludes that he should have let Sai play all the games instead of playing all of his games on his own, and vows never to play Go again. He does not show up for pro games for a couple of months until his friend Shinichiro Isumi, looking to re-take the pro exam which he has previously failed, insists on a game with him. During play, Hikaru suddenly realizes that Sai has actually been with him all along, through the style of playing he picked up from him.
With renewed vigor, Hikaru returns to the world of Go. Still considered a 1-Dan player (the lowest rank) because of his long absence from the game, he faces Akira in another match and loses, but his play has clearly improved from the last time they played, and they acknowledge each other as friendly rivals. The anime ends after their match (although a 90-minute special was produced in 2003 to include some of the following events), but the manga continues. They play each week at a Go salon, where others are surprised that Akira is spending so much time with a mere 1-Dan. Exasperated, Hikaru declares that he and Akira will face off in an official match. He believes he can eventually achieve the Divine Move.
Hikaru plans to enter the Hokuto Cup, a tournament for under-18 Go pros. As the highest-ranking under-18 pro, Akira qualifies for the tournament but Hikaru has to play a series of games to become one of the three Japanese competitors. His friends Waya and Ochi also enter the qualifying matches. He meets Kiyoharu Yashiro, a player from the Kansai (Western Institute), whose style is as strange and offbeat as his own.
Hikaru, along with Akira and Kiyoharu Yashiro, are selected to represent Japan, while Hong Su-Young (a Korean Go player who was beaten by Hikaru earlier in the series) and two others represent Korea and three of Shinichiro Isumi's Chinese friends represent their country.
The captain of the Korean Go team, Ko Yongha, is interviewed and his remarks translated for Japanese viewers. The translator makes an error which causes it to appear that he is disparaging the skill of Hon'inbo Shusaku, who, like Hikaru, was possessed by Sai. Although Yongha later finds out, he refuses to correct the error and instead emphasizes it when he realizes that it enrages Hikaru, who takes it as a direct affront to Sai. This leads to Hikaru eventually challenging the captain; he loses by only half a moku(point).
Japan eventually comes in last, behind Korea (1st) and China (2nd).
In the end, Hikaru is asked his reason for playing Go. With tears in his eyes, he answers "To link the far past, with the far future". The manga then ends cyclically, with Sai's ghost once again asking "can you hear my voice?"