Now head of the Kurokami Group, Medaka Kurokami withdraws from Hakoniwa Academy. After fourteen years together, the time has come for Medaka and Zenkichi Hitoyoshi to part ways. But first, a flower filled send-off party for the president who loved flowers! Zenkichi arranges a 100 Flowers Run for Medaka; a battle against one hundred opponents from her academic year. Medaka defeats Zenkichi first at the base of the clock tower, and after traversing the academy to collect flowers from her opponents, faces Misogi Kumagawa last at the top of the clock tower. He reveals that each flower includes a farewell message from each of her opponents. In April, at the beginning of the school year, Medaka returns to the academy as the new chairwoman.
A Flower Filled Send-Off
Medaka hands in her withdrawal notice to Hakama Shiranui. He questions if she won't change her mind, but accepts her decision. Zenkichi is shocked to hear from Youka Naze that Medaka is leaving the academy. Namanie Nienami shows up in the Student Council's office as they discuss Medaka's upcoming departure, much to Zenkichi's annoyance. He worries how Hansode Shiranui will react, only to find she has already heard from Kamome Tsurubami. Shiranui vents her anger, promising to stop Medaka with all her strength. As the Student Council ponder how to convince Medaka to stay, they are interrupted by their faculty advisor, Messhi Kuguhara. He warns them against trying to force Medaka, labeling his as an adult's opinion. After stepping out of the office, he confronts his fellow faculty members. The others look to Zenkichi as to what they should do. Zenkichi decides to speak with Medaka directly. He finds her cleaning her classroom. Medaka tells him she wanted to wear the proper uniform once before leaving. She excitedly tells Zenkichi about her future work for the Kurokami Group. Zenkichi is relieved to see that she is happy with her new future. Medaka then asks him if he is packed yet, fully expecting him to accompany her. Zenkichi is momentarily thrilled, then refuses, citing his responsibilities as Student Council president. Medaka is shocked by his rejection. The two say good-bye, then Medaka leaves to cry in private. As she exits, she asks Zenkichi to hold a farewell party so she can say good-bye to everyone else. After Medaka leaves, Zenkichi orders Nienami out of hiding. Nienami steps out of a locker, wondering why Zenkichi refused Medaka's invitation to come with her. Zenkichi tells her that he has decided to change himself, and for Medaka, they will throw the very send-off party Najimi Ajimu once thought up as a joke.
Following a series of puzzles from Zenkichi, Medaka arrives at the clock tower to find him waiting for her. She correctly deduces that the puzzles were simply to buy time. Zenkichi is disappointed by how easily she saw through his motives. Zenkichi explains the nature of Medaka's farewell party: a battle against one hundred of Hakoniwa's strongest, the 100 Flower Run. Medaka is thrilled to hear what she will have to do. Asking about the rules, she learns that guests from outside the academy have been invited, and that she will have ninety minutes to finish. After explaining the rules, Zenkichi removes his glasses and approaches Medaka, admitting that there is a part of him that wants her to stay. Raising his fists, he asks her to beat that part out of him. Medaka admits that there is also a part of her that wants to stay, and knocks Zenkichi down with a swift uppercut. As she runs off with his flower, number seventy-three, Zenkichi laments to himself that she has left him behind again. Smiling tearfully, he bids Medaka goodbye. Carrying a duffel bag over her shoulder, Medaka heads to the nearest building, to find over twenty students awaiting her. Introduced by Habataki Hyūga as the small fry characters army, Medaka insists there are no small fry characters at Hakoniwa. Entering End God Mode, she readies her Kurokami Final. Using Kurokami Final, Medaka blows the assembled students away. The group have mixed reactions, but all present wonder if Medaka thinks of their time together as good memories. Medaka cuts her hair and takes tally of her flowers. She decides to move on to the strong, easy to find opponents early. In Class 13's homeroom, Medaka finds the entire Thirteen Party, her brother subbing in for Myouri Unzen. She smiles at the prospect of fighting them all at once. Moving on to the Ghost Babel, Medaka fights Class -13 students Gagamaru Chougasaki and Shibuki Shibushi. She next finds the Student Committee Chairman. She is unsurprised to see Tokemichi Choujabaru subbing for Kiruko Tachiarai, noting that Tachiarai hates her. Choujabaru explains Tachiarai meant to join in, but overslept, forcing Choujabaru to hold flower number fifty-two and participate in her place. Changing her uniform, Medaka charges. In the chairman's office, Medaka meets several members of the academy faculty and her own family. Kajiki Kurokami tells Medaka that she can still ask not to be the group head if she does not want to be. Nashi Kurokami tells Medaka that she is participating as a representative for Hato Tsurubami, and holds flower number thirty-six in her place. After speaking with her father and step-mother, Medaka tells them to rise; the adults insist they do not need to stand to fight with a child. Afterward, a worn Medaka estimates she has fifty-eight flowers, but notes she has used up half her time. She runs into the entire Shiranui family, as well as Iihiko Shishime.
Medaka uses her various God Modes to defeat Iihiko and the Shiranui doubles, as well as ninety-nine trample skills against Kairai Kugurugi. After Medaka defeats Kairai, Gizou Yuzuriha pulls down her skirt; Medaka sends him flying with a kick. In the face of Shiranui's Real Eater, Medaka whispers to the other girl, before running off with the Shiranui family's flowers. Asked by Obi what Medaka said, Shiranui tells Obi that Medaka asked her to enjoy her youth. Medaka comes across Nekomi Nabeshima, who hands over her flower without a fight, telling her their fight will have to wait fifty years. In the library, Medaka finds the Language Users and Bukiko Udou. Namanie Nienami makes herself out to be the group's leader, annoying the others. Kamome Tsurubami tells Medaka that, having found his father, he now wants to find himself. Momo Momozono tells Medaka they will play with words, challenging her to a game of "Rolling Match Point". In the Student Council office, Medaka is surprised to see members from several generations of the Student Council present, as well as her sister, who she has already fought. Mogana Kikaijima tells Medaka that "Youka Naze" and "Kujira Kurokami" are two different people, and that Kumagawa is participating, but wanted to fight her alone. Kouki Akune tells Medaka that they will be going all out against her; Medaka relishes the prospect of fighting all of them. In the Public Morals Committee's office, Medaka finally meets Unzen, as well as several other Enforcers. She is surprised when Unzen introduces his sister as his successor, who is now speaking (haltingly) in proper language. The group attacks her all at once, led by Unzen. Medaka confronts Kumagawa on the top of the clock tower, noting that it is just like him to be waiting at the starting place, and telling him she still needs two more flowers. Kumagawa explains to Medaka he possess a flower of his own, as well as flower number four, in place of Ajimu, making him her last opponent.
Facing down Medaka, Kumagawa goes on to explain that Ajimu passed him a message for Medaka when she returned Hundred Gauntlets and granted him Unskilled. He then points out to Medaka that the card with each flower she has collected is made of two parts. Medaka is surprised to discover what each flower includes; a message from each of her opponents. Medaka is overwhelmed by everyone's messages, but Kumagawa tells her just to accept them. Medaka composes herself and prepares to fight Kumagawa, thinking that Zenkichi managed to surpass her in the end. Readying his screws, Kumagawa tells Medaka to come at him with all she has, stating he will not be satisfied with just one win. As the narration details Medaka's time as Student Council president, Medaka charges forward with a smile. Come April of the new school year, Zenkichi greets the new students by making a speech at the entrance ceremony. He is shocked to see the academy's new chairwoman is none other than Medaka. Naze explains that her sister took over the position from her father's double, Hakama. Three new freshman approach the stage and attack Medaka, despite Zenkichi's warning to run away. Medaka defeats them instantly, and welcomes them to Hakoniwa Academy.