When Yuki Miyata is hopsitalized with an illness, her best friend, Minami Kawashima, offers to take her place as manager of Hodokubo High School's baseball team, despite the fact she hates baseball herself. She buys Management: Tasks, Resposibilities, Practices by Peter Drucker which she later discovers is about business management as opposed to managing a baseball team, but Minami nonetheless becomes intrigued by its contents. Deciding that she first needs to 'define what the team is', she talks with Masayoshi Nakai, who hopes to become the team's CEO someday. Later, Yuki recalls a memory on how moved she was when Minami scored a winning bat during elementary school, which inspired her to join the baseball club. Having determined what the goal of the club is, Minami's decides to move onto the next step: Marketing.

Despite showing some initial improvement, Minami notices the team being less motivated following a week of exams, with many members skipping practise. After school, Minami encounters Yūnosuke Sakurai opting for karaoke instead of practise, saying he's not worthy to be on the team following some of his slip-ups in the previous game. Looking to Management, she looks into 'consumerism', believing the absensees to be a form of boycott against the way they practise. Minami and Yuki ask Ayano for her help, who determines most players who only show up for games because of its competitive nature compared to practise. With this information, she and Makoto set up a new training exercise focused around teams and points which encourages the players to be more responsible and strive to improve themselves.

After just losing an exhibition match, Masayoshi, who is a little downhearted about not being in the starting lineup, feels that both he and the team need to change to make it to the nationals. Minami makes some suggestions to Masayoshi after reading about 'Innovation' in her book, before being harshly reminded about the promises she made to the other clubs who approached her. After talking with fellow teammate Jun Hoshide, Masayoshi decides to join the management team. Later, the team works on joint exercises with some of the other clubs Minami helped out with to mutual benefit. Later, as Masayoshi discusses innovation to the other managers, Minami suggests that Makoto aim to revolutionize high school baseball like other coaches before him. As an exhibition is being set up, Makoto reveals his innovative idea; the "no-bunt, no-ball" strategy.

As the team work on their strategy, designed to reduce the time the pitcher spends on the field and encourage defense, Minami learns Yuki is due to undergo surgery on the day of the exhibition match. It is revealed that Minami used to love baseball when she was little, but as she grew older, her hopes of becoming a professional baseball player were dashed. The exhibition match goes underway, with the team implimenting their new strategy to only aim for strikes. Whilst the match appears one-sided, the team notices their improvement as the game goes on. After managing to improve on defense, they start to impliment their no bunt strategy on offense which takes the other team by surprise. Despite losing the game, the team feels proud

With new members joining the club and more responsibilities piling up, including evaluations on the other players, Minami decides to impliment 'top management', splitting the various tasks amongst herself, Masayoshi, Ayano and Hanae. Minami becomes concerned that the growing number of applicants will result in many players never seeing the field, as well as leaving some of the other clubs empty-handed. She decides to focus on 'optimizing', interviewing each applicant and reducing them from 30 to 12 based on why they want to join the club, whilst reccomending those who didn't make the cut to other clubs, though she forgets about the evaluations in the process. After thinking about her observations and the interviews, Minami and Makoto manage to decide on a starting lineup for the upcoming tournament, appointing Masayoshi as the team captain.

The tournament begins, with the team winning their first five games thanks to their 'no bunt no ball' strategy, earning them a place in the quarter-finals. Afterwards, Yuki gives her thanks to Minami for all the courage she had given her the past year, though feels downhearted when Minami appears to put more focus on results than the overall experience. As the team start to struggle in the quarter-finals, Minami has the crowd sing Keiichirō's favourite song to give him encouragement, and the team make a comeback, winning thanks to the pinch runner, Fumiaki Kutsuki.

Hodokubo faces off against Shuuhoku in the semi-finals, whose pitcher is one of the most fearsome and has a rivalry with Jun. As the score remains tied up until the last inning, Jun manages to hit a home run in the last inning. As they try to defend their point, Yūnosuke makes a few mistakes, leading to the bases getting loaded, but thankfully the support of his team help them knock out the other players and win the match. As the management team discuss taking Yūnosuke off the starting lineup, due to the mistakes he makes under pressure. Minami insists that he kept in for similar reasons to Keiichirō. However, as Minami goes to the hospital, she learns that something terrible has happened to Yuki.

Yuki's condition takes a turn for the worse and she is put on life support, with nothing more that can be done to save her life. As Yuki's mother brings everyone to say their last goodbyes, Minami can't bear the bad news, wanting Yuki to fight through it, but her mother reveals that she had been fighting for a whole year despite being expected to only have three months to live. Minami feels guilty about the last thing she had said to Yuki before the quarter finals. Yuki passes away by the morning of the finals and Minami becomes angry, believing everything she has done has become pointless and blaming herself for making Yuki suffer for so long. As Minami reveals her hatred for baseball, it is revealed the team already knew having been told by Yuki. Conflicted, Minami runs off, but Ayano catches up to her, bringing her back to the stadium as the team are down 4-0. Overcoming her fears, Minami begins to cheer her heart out for her team.

With encouragement from Minami's cheers, the team start making a comeback making the score 4-3 as it comes to the last inning. With Yūnosuke forced to make the definitive bat, he makes the same play that Minami once did when she was younger, the play that inspired Yuki to love baseball, allowing the runners to reach home and clinch the match. As the team celebrate their victory, Minami has a vision of seeing Yuki, remembering all the good times they shared together. With the memories of Yuki in their hearts, the team moves on to the nationals, hoping to play baseball the way the customers want.