It is revealed that Naze is the successor of Maguro as the supervisor of the Flask Plan. Koga tries to grapple Akune, but he temporarily dislocates her arm in response. After Maguro vaguely hints to Akune about his options not being limited to destroying or not destroying, Akune pins and holds Koga to the ground to exhaust her, deducing that her weakness is fatigue. Maguro tells Naze to remove her bandages from her face, and after Naze surrenders her two flash drives containing data on the Flask Plan to retrieve Koga, Maguro recognizes Naze as Kujira Kurokami, his long-lost younger sister. In the past, Naze isolated herself in her room and only concentrated on her studies in biology, but she left the house on her eleventh birthday and was never heard of again ever since then. In the present, Maguro admits that he formerly joined the Flask Plan all to find Naze for six years, since he cares so much about her. When Maguro finally embraces Naze, she incapacitates him using a syringe. As Naze changes her mind about giving up her research, Medaka suddenly burst through the wall and reunites with her older sister.
Harigane Onigase, a member of the disciplinary committee, enters the student council office and exploits the student council members for their violations of the dress code. Onigase leaves in anger after Medaka chooses to ignore this. Although Zenkichi tries to persuade Onigase to let this go, Onigase uses the suggestion box to her advantage, anonymously requesting Medaka to find an object inside a dirty outdoor swimming pool, assuming she would change into a swimsuit. Instead, Medaka jumps into the swimming pool with her uniform on, which then Onigase is taken by surprise and also jumps into the swimming pool in guilt and shame. Later, Onigase accidentally handcuffs Zenkichi after scolding Shiranui for eating donuts in the hallway. As Zenkichi and Onigase head to the disciplinary committee office to get the key, they chance upon Medaka, who inadvertently handcuffs Zenkichi as well. After they help various students in need of assistance, they are ambushed by the Mokkin Team, a pair of delinquents who use their wooden and metal baseball bats to attack. Medaka and Zenkichi destroy the baseball bats with their kicks and cause the Mokkin Team to flee, giving Onigase a whole new insight on the student council.
The rule of the judo match is that Zenkichi must score one point before Akune scores ten points. Nabeshima wagers with Medaka, offering Akune to join the student council in exchange for Zenkichi to join the judo club. In response, Medaka cheers for Zenkichi, allowing him to win the match. As Betsuhei Jounan has taken over as the new captain of the judo club, Nabeshima relieves Akune from the judo club so he could chase his dream to win Medaka's heart. Zenkichi is distraught upon learning that Akune is now the secretary of the student council. Medaka tasks Akune to help Kenna Yatsushiro, a tomboy with bad handwriting, to convey her feelings for a crush in a love letter. When Akune gives Medaka a rough draft of the love letter, Medaka comments that Akune was only using his own words rather than considering Yatsushiro's feelings in the matter. With that in mind, Akune decides to tutor Yatsushiro in handwriting skills, and after a week of practice, Yatsushiro finally gives the love letter to her crush. Medaka takes back what she said earlier and thanks Akune for his hard work.
Shiranui bails out on Zenkichi, who is forced to bow down to Oudo. Mizou Yukuhashi spots Medaka, who is also subdued by Oudo. When Oudo proposes to Medaka, Zenkichi tries to attack, but Yukuhashi intervenes. After Oudo requests Medaka to meet him atop the clock tower at five o'clock the next morning, Zenkichi soon notices that Medaka may have developed feelings for Oudo. However, since Oudo is posed as a new threat, Medaka wants to become stronger. Medaka and Zenkichi go to an old administration building to visit her older brother Maguro Kurokami, who seems to be obsessed with her. After Medaka demands Maguro to train her and tell her about the Flask Plan, he shows them his surgical scars of being a failed experiment in the Flask Plan, but he does not give any information regarding this project. After Maguro sees how determined the two are in becoming stronger, he decides to train them both.
The second event is the underwater three-legged race. Zenkichi and Akune race each other and end up in third, Ariake and Isahaya place in second, while Umumichi Yakushima and Sotsu Tanegashima easily finish in first. The third event is the underwater eel catching. Nabeshima catches nine eels but still is in ninth overall, Mogana Kikaijima catches thirteen eels and lands in first overall, while Medaka was unable to catch any eels and is brought down in eighth overall. After hearing the swim team declare that they would die for money, Medaka makes it her mission to rehabilitate them. The final event, chosen by Shiranui and Aso, is the underwater cavalry battle. During the battle, Kikaijima expresses desperation for money due to childhood struggles. Zenkichi and Akune toss their inflatable armbands out when Kikaijima pushes Medaka into the air. This allows Medaka to safely land above water, and she tackles Kikaijima with a kiss, thereby winning the match. However, the judo club wins the inter-club aquatic meet by a landslide, since they managed to grab the bandanas from the other teams while Medaka and Kikaijima were distracted by their match. Kikaijima is then appointed as the treasurer of the student council.
On the thirteenth floor resembling a computer room, Medaka declines Oudo's offer yet again to be a part of the Flask Plan. Koga, feeling insulted due to the fact that she was made into an android for this project, believes that Oudo is not strong enough to defeat Medaka, but Oudo reaches inside Koga to take her ability. Naze is left in tears after seeing Koga in critical condition, imploring Maguro to tend to Koga's wounds. During the match between Medaka and Oudo, the latter notices that the former has acquired abilities from her past opponents. However, Medaka is actually able to control and master these abilities at will without any problems. When Oudo tries to claim Medaka's power, he falls back after seeing the darkness which lurks inside of her. Medaka makes Oudo change his ways and apologize for his actions. When everyone ride on the elevator to the first floor, they are shocked when both the Loser Team and the Plus Six are wiped out by large screws, and the person behind this happens to be Kumagawa.
Najimi Ajimu, founder of Hakoniwa Academy (or Sandbox Academy) and creator of the Flask Plan, introduces this episode as a direct sequel to the manga's side-chapter of the same name which follows Kumagawa, an extremely formidable Minus wreaking havoc with his large screws as the president of the student council at the prestigious Suisou Academy (or Fish Tank Academy). Saki Sukinasaki runs late for school and is reluctant to find out that her hair was bleached somehow. She informs Kumagawa of this and deduces that Fude Ezumachi, who has the ability to manipulate color with his art, is responsible for this. Kumagawa confronts Ezumachi, who eventually splashes blue paint on Kumagawa to restrict him. Later, as Kumagawa recovers from an epiphanic dream about Ajimu, he gains the resolve to defeat Ezumachi. As Kumagawa and Sukinasaki head to the football field, they discuss that Ezumachi was in love with Aki Jakago, the former president of the student council. Kumagawa confronts Ezumachi again, this time removing the twelve basic colors from existence, in which only white and black remain. Kumagawa pierces through Ezumachi with large screws, saying that life and death have no meaning, just like the colors white and black.
Medaka believes that she has come to her senses and must be a part of the Flask Plan to achieve perfection, much to the disagreement of Zenkichi, Akune and Kikaijima. After she subdues the three, Maguro notices from a distance that Medaka is shedding tears despite her being heartless. Zenkichi fights back with his kicks and tries to get Medaka to remember her true self. In the past, Medaka's mother died after giving birth to Medaka fifteen years ago. During her first two years of life, her ability to surpass the intelligence of adults at such a young age made her realize that life and death have no meaning. In the present, after recalling her first encounter with Zenkichi thirteen years ago telling her that she was born to make everyone happy, Medaka rips out of her straitjacket and punches Zenkichi, realizing that her new purpose in life is to protect herself. She strangles him until she realizes that he remembered what he told her back then, which causes her to yell in agony. Zenkichi embraces Medaka, telling her that she must include herself in her purpose to make everyone happy, which then reverts her back to normal.
Naze, who repressed her childhood memories and exhibited stoic behavior as a result, tries to attack Medaka with a green syringe, which contains a poisonous liquid. Medaka demands for the antidote but first injects herself with the green syringe, which only weakens her body. Naze then gives Medaka an orange syringe to inject, seemingly containing the antidote, but it suppresses her memories and purpose in life. Before Naze and Koga leave with an unconscious Medaka in tow, Naze tells Akune and Maguro that she plans to change Medaka's personality as her final experiment. Akune and Maguro meet up with Zenkichi and Kikaijima to inform them of the situation. Harigane Onigase, Myouri, Nabeshima, Myouga, Takachiho and Munakata, who make up the Loser Team, all arrive to offer a helping hand, but as they all head for the elevator to go to the thirteen floor, they are stopped by the Plus Six. The Loser Team faces against the Plus Six, while Zenkichi, Akune, Kikaijima and Maguro use the stairway down to the twelfth floor resembling an arcade. However, Yukuhashi stands in their way to prevent them from interfering with the experiment, which will be over in fifteen minutes.
After the training session, Medaka and Zenkichi meet Oudo atop the clock tower on time. Zenkichi kicks Oudo off of the clock tower, but the latter is able to grip against the side of the clock tower while still standing. Oudo explains that the Flask Plan is a project intended to involve all of the academy students, using a formulated potion which may grant superhuman abilities, but only a small percentage of academy students will be able to survive the experiment. Although Medaka vows to stop the Flask Plan from happening, the suggestion box is soon stuffed with requests related to Class 13 and the Flask Plan. At the underground laboratory beneath the clock tower, twin brothers Sanou Tsushima and Unou Tsushima, who guard the Door of Rejection, are amazed when Medaka and Mogana Kikaijima each enter the correct security code to pass through. However, since that security code is no longer valid, Kouki Akune smashes through the door, allowing him and Zenkichi to catch up with Medaka and Kikaijima. As they enter the first floor resembling a labyrinth, Shigusa Takachiho stands in their way, but this may be an opportunity for Medaka to test her newfound strength.