Saki Miyanaga is a skilled mahjong player, but she hates the game since she would be punished by her family whether she won or lost when she played with them. Upon entering high school, Saki's friend, Kyōtarō Suga, takes her to their school's mahjong club so Saki can be a fourth player. There, she meets Nodoka Haramura, a very skilled mahjong player and previous junior high champion, and Yūki Kataoka, an energetic first-year who is skilled in mahjong though has trouble staying focused. Saki only plays a few hands and leaves shortly after the club president and student council president, Hisa Takei, wakes up. Hisa notices Saki managed to keep her score at zero, a difficult feat. Hisa manages to get Saki to come back the next day to play a couple more games with Nodoka, Yūki, and Mako Someya, a second-year member of the club. Saki shows her skill in mahjong by attaining the zero score in the first game.

Playing under special scoring rules, Saki plays the next game while trying to keep her plus/minus zero score and winning at the same time, but cannot do both with the special rules. However, when the special rules are removed, Saki ended up winning the game, therefore disallowing her from keeping the zero score. Nodoka is dejected after losing since before Saki told her that she hated mahjong and despite that won, but Saki tells her that playing with her was fun. Saki thinks about what Nodoka said, and even tells her father that she wants to one day play again with her mother and sister like they used to before they left to be professional mahjong players. The next day, Saki joins the club, saying that she wants to play more and win against Nodoka.

It has been a week since Saki joined the mahjong club, though Nodoka is still distant to her. Nodoka plays a game by herself with all the tiles exposed and takes notes, but she is still unable to attain a plus/minus zero score like Saki who can do this flawlessly. Hisa and Mako go and sign up their club for the national qualifiers for high school students. Saki wins a game against Nodoka, Kyōtarō, and Yūki, who is depressed that she cannot possibly win when playing against both Saki and Nodoka. In the next game, Saki lets Yūki win, which makes Nodoka angry since while Saki did it so that everyone can have fun, Nodoka can only have fun when Saki is playing at her best. Saki makes a promise with Nodoka to shoot for the nationals, and the two finally become friends.

Hisa announces to the club that they are now signed up for the national qualifying tournament, and she hands out the rules. Yūki sees that one school, Ryūmonbuchi, are extremely skilled and even won the tournament the previous year despite being all first-year students. Hisa asks Saki and Nodoka to help out at Mako's family's cafe, telling them that learning about the real world is also important to improve their mahjong skills. When they arrive at the cafe, they see that it is actually a maid cafe, and they have to wear embarrassing maid uniforms. Patrons can also play mahjong there, and Saki and Nodoka easily win against two customers. After one leaves, a woman who Saki is intimidated by joins them. The woman completely mops the floor with them, and at the end it is revealed that she is Fujita, a professional mahjong player. Saki and Nodoka later find out that Hisa set the whole thing up so that they could also feel what real defeat is like. Hisa explains that the club is going on a training camp to improve their skills.

The mahjong club goes to a mountain retreat training camp to improve their skills. The first day is spent mainly having fun, and playing some normal games of mahjong. The next day, Hisa gives the first years (excluding Kyōtarō) special tasks. Saki plays mahjong online, but is dejected how easily she loses to others. Nodoka has to gain experience playing others in real life when she is more skilled playing online like she is used to when playing at home. Yūki does math drills in order to improve her ability to keep track of the score when playing mahjong. Afterwards, Yūki becomes depressed how she loses so much against Nodoka, Saki and Hisa, and the club president recounts how when she was a first-year, she was the only member of the club, but she kept with it and now she is grateful there are many new members. Yūki continues to play, and manages a win. The next day, Yūki, Nodoka and Saki go to see the nearby waterfall.

After arriving at the tournament area, Saki gets separated from her friends, and during this time Nodoka gets hounded by reporters due to her having won last year's national junior high school tournament. After Saki makes it back to the others, Hisa explains the order of the players, starting with Yūki, followed by Mako, herself, Nodoka, and finally Saki. While initially underestimated by her opponents, Yūki wins many hands, nearly shutting out the others. Afterwards, Mako and Hisa also make quick work of their opponents, ending with a commanding lead. When it is Nodoka's turn, more people show up to watch her match.

Nodoka walks into her match holding her penguin stuffed animal which causes a stir among the observers and her own opponents. Nodoka plays extremely well, and of the competitors from Ryūmonbuchi, Tōka, notices her similarities to a famous skilled online mahjong player known as Nodocchi. She tries telling this to her teammates, but they still do not think it can be true. Saki makes short work of her round by taking the remaining points from one of the players, and the team progresses on to the semi-finals round. In the semi-finals, Saki's team makes it through to the finals, along with Ryūmonbuchi, Kazekoshi, and Tsuruga Academy. One of the members from Kazekoshi, Kana Ikeda, gets harsh treatment from their coach for not playing up to her expectations, despite the fact they made it to the finals. The captain of the the team, Mihoko Fukuji protects Kana, and after the coach leaves, the captain encourages her teammates in showing everyone that their school is the best.

The Kiyosumi team takes the train back to town since they do not have enough money to stay in a hotel near the tournament. Hisa tells Mako how she was the reason why Hisa held on to the hope that more girls would join the mahjong club the next year so that they could go to the prefectural tournament together. Nodoka recounts to Saki how she used to play mahjong only on the Internet due to lack of players, but after entering junior-high school met Yūki and others, leading them to enter into the junior-high tournament, though only Nodoka advanced. The girls from Kazekoshi talk about how their captain, Mihoko Fukuji, does most of the work for the club, and since it is her last year, they want to play as hard as they can so they can go to the national tournament. Tōka dispatches a butler to bring Koromo Amae to the tournament, who had been sleeping all day.

The final's first round starts when Ryūmonbuchi representative Jun Inoue accidentally eats Yūki's only taco. The latter cries and causes a commotion, but Mihoko shares her lunch box with her. As the game progresses, Jun starts to win many hands and pressures Yūki who is gradually losing her confidence. Mihoko opens her right eye and uses her power to read the game's flow in order to help Yūki gain her points back from Jun. Jun gets irritated over the two teaming up against her while Yūki thinks Mihoko is her ally. However, Mihoko surprises everyone with her continuous winning, and both Jun and Yūki finally realizes that she is the true enemy. The first round ends with Mihoko completely dominating the game points for the Kazekoshi team.

Hisa recommends Saki and Nodoka take a nap before their matches, and while Nodoka initially declines, she decides to go so that Yūki does not have to cry in front of her and Saki following her match. Mako's turn comes up, and Hisa explains that she takes off her glasses in order to remember past matches she had witnessed.

The third round starts and Hisa puts to work her strategy of sticking to the bad waits in order to get the big scores, knocking off Kazekoshi's lead. Hajime Kunihiro helps gain a slight comeback while avoiding her slight-of-hand habit. Meanwhile, Nodoka wakes to find that her penguin is missing and leaves Saki to go look for it.

Mihoko arrives to pass along the information to her companion, and Hisa barely recognizes her. Koromo takes the torn penguin to her butler, who fixes it, and she returns it to Nodoka. While Nodoka expresses her gratitude, she leaves quickly and is unable to hear Koromo's name.

The fourth round begins off slow with Nodoka winning a small hand, and as play continues, the players continuously keep on getting draws. Eventually, Nodoka is able to get more into the game, and ups her skills like when she is playing online. By the time of the last hand of the first half of the round, only Nodoka has won any hands and has pulled ahead of the other three.

Tōka makes a slight comeback, ruining Nodoka's perfect run, but then falls into a play laid by Tsuruga's Momoko Tōyoko, whose presence is so small her calls for riichi cannot be heard by her opponents. She had trouble being noticed and had abandoned all communication until she was found by her school's mahjong club leader, Yumi Kajiki.

Momoko's abilities fall short against Nodoka, whose training matches her real life playing to her online play style, therefore not taking notice of Momoko's lack of presence. The round ends with Kiyosumi retaining the lead. The final round starts with Saki, Kana, Yumi and Koromo, though initially Saki cannot connect the fearsome aura she felt with the petite looking Koromo.

As the round continues, Saki finally recognizes Koromo's aura. She starts putting pressure on her opponents by reducing their tenpai probabilities and playing two haitei raoyue moves in a row. However, this is broken up when Yumi allows Saki to win with a her discard. Yumi then follows this up by getting some points from Kana.

During the break, Mihoko goes to comfort Kana, and Nodoka catches up with Saki to reaffirm their promise and rebuild her confidence. Fujita warns Koromo to play mahjong properly.

Remembering the pact she had made with Mihoko, Kana gets a burst of confidence and regains a lot of points. Yumi also gets a good play, and Koromo, having paid all her attention to Saki, gets a little agitated. Saki takes off her shoes and socks, remembering the times she played mahjong at home and at the training camp.

Koromo recalls that when her parents died, no matter how many times Touka brought her friends, she still always felt lonely, believing her only worth is in mahjong. Koromo's powers cause a brief blackout, but Saki remains calm throughout. Koromo gets another haitei raoyue once the game resumes, leaving one more hand. Koromo is a bit shocked when Saki says she is having fun playing against her.

As a reward for winning the tournament, and to train for the individuals, Hisa takes everyone to a pool, where Saki admits she cannot swim. They run into the Ryūmonbuchi group, who actually own the pool, and Koromo makes friends with Nodoka. Tōka reminds Koromo that when she went to Tokyo with her group, and went to a family restaurant, that reminded her of her parents. Meanwhile, Kazekoshi and Tsuruga make their plans for training for the individuals. Saki's sister, Teru, progresses to the nationals, though when asked about Saki, denies her existence.

The first day of the individuals tournament begins. Tōka faces off against Tsuruga's Kaori and is beaten by her beginner's luck. Another Tsuruga girl informs her team mates of an opponent who was strong during south winds. Despite pressure from being the team champions, Kiyosumi manage to get through, though Kyōtarō, who had been participating in the boys tournament, is knocked out. In the second half, Mihoko ends up facing against Hisa, who still does not remember her. With Hisa ahead, Mihoko decides to use her right eye to win the game. Hisa finally remembers who she is and Mihoko gets her long awaited conversation. The first day ends with all of Kiyosumi's players progressing. Yūki, who had a winning streak all day, psyches herself up for the next day.

It is the second day of the individuals, and Yūki is shocked to find the day will consist of east-south round games. Yūki gets off to a good start in her first match, but when the south wind approaches, Kazue Nanpo from Hirataki High School shows off her field advantage and wins the game. During the midway point, Nodoka is shocked to find Saki has gone back to her habit of scoring plus minus zero, and goes to confront her about it. Saki had been holding back since it was Hisa's only chance at the individuals, but Nodoka reminds her that their promise included not holding back. Saki ends up in a match against Hisa, as well as Momoko and Tomoki. Hisa immediately concocts a strategy to seal off Saki's rinshan kaihō strategy, which eventually convinces the others to gang up on her. Later on though, Momoko, determined to avenge Yumi's earlier lost against Saki during the team tournament, decides to implement her stealth tactic in order to win.

Momoko continues to put the pressure on Tomoki and Hisa keeps racking up strong plays, while Saki is still unable to use her usual strategy. Saki remembers her training using online gaming, and uses what she learned to pick out Momoko's tiles, finally allowing her to play a rinshan kaihō to win the match. In the final round, Hisa goes against Mihoko, Tōka and Yumi, Nodoka goes against Kana, Jun and Hajime, Yūki goes against Mako, Tomoki and Momoko, and Saki goes against Kazue, Kanbara and Yoshitome. As everyone battles their hardest, Yoshitome does well to block off Saki in the east wind round, but soon the south wind round comes and Kazue starts to make her move. However, Saki retains her smile and pulls out more rinshan kaihō moves to win her match, placing third and qualifying for the nationals. Nodoka wins her match and qualifies in second and although Hisa wins her match, Mihoko is overall first place.

Kyōtarō tells Saki about an upcoming summer festival and she invites the rest of the club to go too. Hisa sends out invitations to the other schools to join them for Kiyosumi's training camp for the nationals. Yūki ends up flunking her math midterm and has to take a makeup test, failure of which means she will not be able to attend the camp, so Saki and Nodoka decide to help her study. Hisa prohibits them from using the club room and they end up having trouble finding other places to study. Ryūmonbuchi and Tsuruga send their responses for the camp, while Mihoko delivers hers to Hisa personally. After Yūki's makeup test, the club members go to the festival, and Hisa watches from afar with Mihoko. Yūki passes her makeup test and all the schools go to the training camp.

All the schools gather for the training camp where Yumi gives Hisa some data on the other opponents in the nationals. Later on, nearly everyone takes an interest in ping pong while Mako and some others fail to get revenge on Kaori's beginner's luck. The next morning, some of the girls go in the onsen to discuss the powerhouses of the nationals, including Saki's sister, Teru. Hisa's suspicion of Saki as Teru's younger sibling was confirmed by Saki's reaction when she confronted her of this fact. Saki is a bit shocked to hear from Mohoko that Teru had denied having a sister, so Nodoka decides to take her to a shrine to cheer her up. Afterwards, they exchange souvenirs and decide to call each other by their given names. After they get back, the training starts in a room where the players from Kiyosumi, Ryūmonbuchi, Kazekoshi, and Tsuruga are already seated and ready to play, with Hisa also having invited Fujita to join them. Kiyosumi prepare themselves for the nationals.

Nodoka Haramura, Yuuki Kataoka, and Saki Miyanaga go back to the baths to see a shooting star. After Saki leaves to go get some milk, Nodoka and Yuuki begin discussing various things like how the began playing mahjong. Things start to take a turn as Yuuki begins sexually harrassing Nodoka. This situation makes Nodoka accidentally reveal that she is falling in love with Saki.

Miharu Yoshitome recounts her first days in Kazekoshi's mahjong club. She had to work hard to get into Kazekoshi and join the mahjong club. When the first years were having a competition, she met Kana Ikeda and greatly admired her. Later during a match, Mihoko Fukuji notices that something is wrong with Miharu's eyesight.

Tomoki tells Koromo how Touka recruited her to the Ryuumonbuchi team. Two years prior to the current story line, Touka was looking for recruits to join the mahjong team. Hagiyoshi then suggests a "RTS" online player to fill in the last spot. Touka says that she must play against this person to gauge her strength and spends days online in order to verse her.

Satomi Kanbara asks the members of Tsuruga's mahjong club to meet up after school. She then pulls up in her van and informs them that they are going to the beach to help bond with one another in preparation for the prefectural tournament.

After revealing that Kanbara has took a trip with Kaori and Mutsuki to Tokyo, Yumi and Momo decide go on a date together. On the train ride they recount some events prior. Their date consists of playing in the ocean and then staying at an inn.

Kana asks Mihoko if she can go home early to prepare for her sisters birthday party. Knowing that something is wrong Mihoko asks Miharu where Kana lives and then she visits her. She then helps Kana with her sisters party and later comforts her when she is feeling down.

Yuuki Kataoka meets Nodoka Haramura to discuss which high school they might enter. Yuuki informs Nodoka that she will enter Kiyosumi because they serve tacos at lunch and hands Nodoka the Kiyosumi pamplet. When Yuuki jokes that she wants to marry Nodoka, Nodoka says same sex marriage is not a bad idea because two girls can make a baby by using IPS technology. When Nodoka and Yuuki hang out together, they glides over Saki Miyanaga, who is considering entering Kiyosumi.

Bundled with limited special first edition of the 14th volume of the Saki manga.