Sixth grader Hikaru Shindo stumbles upon a mysterious Go board with a blood stain on it. Before he knows it he's hearing voices, one voice to be exact. The voice of an ancient Go instructor, Sai of the Fujiwara. Sai occupies a space in Hikaru's mind. Hikaru is the only one who can see, hear, or talk to Sai. Sai's one and only desire is to play Go. But he can only do that via Hikaru's body. However, Hikaru has no interest in playing Go. Will Hikaru allow Sai to play? And who is this mysterious young boy, Akira Touya?

With the recent defeat of the Meijin's son, Hikaru goes about his day normally. However, Akira is obsessing over the game he lost. He won't do anything but stare at the Go board and replay the game that he lost. When he gets word that Hikaru is at a Children's Go Tournament, he rushes there hoping to confront Hikaru and ask for a rematch.

After loosing the game to Kaga, Hikaru is forced into joining a Jr. high school Go Club Tournament. He is to join Tsutsui and Kaga as the third member for the Haze Jr. High Go Club team for the tournament. But when Hikaru insists that he wants to play for himself, will he come out victorious?

Akira is too good against everyone at Kaio's Go club. The members don't take this sitting down, as three of them plan to take him down.

Akira is still loathed in the Go club, but he doesn't care. Even the club's sensei has bad feelings about him being there. How long will Akira stay in the club?

After Hikaru gets back Yuki's money, Yuki decides to join the club, but refuses to play in the tournament. Tsutsui explains how strong Kaio is and Yuki changes his mind. But will he play without cheating? Meanwhile, Akira discovers that Hikaru is the third board in the tournament and begs the club sensei to put him there. Is Akira willing to give up all his pride and his reputation, just for this one spot?

Hikaru let's Sai play Go online, that way nobody will think Hikaru is really good when in reality he's not.

Akira skipped his first match of the Pro exams in order to play the match against Sai on the net. Akira is perplexed over the identify of Sai which he thinks might be Hikaru while Ogata has his own thinking. Players all over the world are observing the match. Though Akira lost the match, he feels as though he had finally caught up with 'Hikaru'/Sai. When Akira heard from a Go cafe customer that Hikaru was sighted at an internet cafe, he races to the site thinking that he might be Sai. Hikaru denies he's Sai but gets ruffled when Akira seems to disregard him as a opponent. The episode ended with Hikaru saying 'If you keep chasing after an illusion of me, I'll pass by you eventually'.

Hikaru is torn by the decision he has to make. An unlikely saviour came in the form of Kaga who proposed that Shindou quit the club after showing them how strong he is - by playing three of them at once (Mitani, Tsutsui and Kaga). Hikaru prepares to take the Insei exam. Having bumped into Hikaru at the institute, Waya's interest is piqued by Hikaru who declared to surpass Akira and remarked to Isumi that Hikaru will most probably pass the exam.

Although Ouza initally contemplated letting Akira win the match as a form of encouragement, he is angered by Akira's nonchalent attitude and decided to crush him completely. Akira forgot the safer strategy which could have won him the match, in order to show Hikaru his play. While the first snowflakes that mark the arrival of winter fell, Sai muses on the symbolic link between Hikaru and Akira and likened the presence of Akira as being placed there by God to help Hikaru on his path.

HIkaru can't seem to get any better at Go, despite the fact that he plays with Sai every day. If he wants any chance to get into a tournament and face Akira, he needs to get stronger. Sai reveals the ultimate weakness of Hikaru, he's afraid of Sai, and every other opponent he faces.

Yuuki Mitani decides to go back to the Go Club.

Ogata and Kuwabara Honinbou continue their set of matches for the Honinbou title. They are on their final match, both having won the same number of games. When Ogata plays a sealed move for the first time, will he be able to follow up his actions and defeat Kuwabara?

This is a very fun episode where Waya, Isumi and Hikaru form a team to go around challenging the patrons of the various Go salons. The bet being that they won't have to pay the admission fees in event of a win and Waya raises the stakes even higher by allowing a few moku handicap in subsequent games, much to the protests of Isumi/Hikaru (since they have to wash all the stones if they lose). Hikaru becomes friendly with a particular go salon named 'Heart of Stone' and its patrons. Through this exercise, Hikaru manages to overcome his weakness in playing go with adults.

The Pro Exam has finally begun, and the intensity reaches new heights after the pairings are chosen. Everyone seems so tense, except for Hikaru, who is unusually calm. Thanks to Waya and Isumi, Hikaru has learned how to handle the pressure. However, could their actions have turned Hikaru into a real threat?

After losing to Hikaru, Isumi begins to break down and begins losing his matches. Hikaru is also having trouble concentrating, upset about pointing out Isumi's illegal move. As Sai helps Hikaru regain his concentration, Isumi faces off against Ochi. Perhaps this game will be enough to return Isumi to his old self.

The Go World goes into a state of shock after Toya Meijin announces that he is retiring as Professional Go player. As everyone tries to find out why Koyo has given up his titles and his status, Akira begins to worry about Hikaru's progress.

Hikaru discovers that Sai is missing and searches all over him. Unable to locate him, he travels to Inno Island to visit Shusaku's grave in an effort to find him. Is it true? Is Sai really gone?

Hikaru has finally started to play Go again. He has found Sai within his moves, within his Go. But can Hikaru win his first comeback match against 2-dan Murakami? Everyone is watching. Meanwhile, what will become of the Haze Jr. High School Go club? After the year is over, only one boy will be left. Everyone else will graduate and move on.

The match between Hikaru and Akira comes to an end. Hikaru tells Akira that one day, he will tell him everything. At night Hikaru has a dream, with a surprise visitor! At the end, the song “Get Over” is played as we see everyone throughout the series. The Go world is changing and a younger generation has arrived!