Kurokami Medaka is perfect in anything she tries to do – be it sports, exams or anything else. When she ran for Student Council President, she managed to gain 98% of the votes, promising to solve everyone’s problems, 24/7, through the suggestion box that she implemented. Because no-one can match her standards, Medaka runs a one-man Student Council, and so she asks her childhood friend Hitoyoshi Zenkichi to join her, but he isn’t interested. To change his mind, Medaka brings Zenkichi along when solving her first request – to deal with the third-years that have taken over the kendo hall.

A second-year, Ariake-senpai requests the Student Council’s aid for solving the problem of a threat she found in her sports locker along with a ruined set of spikes. Medaka immediately deduces the culprit down to everything but their name from just the letter and the state of the shoes, and goes down to the sports field to catch the culprit. After being outrun by Medaka, Isahaya-senpai denies having touched Ariake’s spikes or making the note, but Medaka believes her immediately, dropping the matter. Feeling guilty, Isahaya takes Ariake’s trainers and replaces them with a brand-new set of spikes and an apology note. When Zenkichi is asked to complete a request to find a lost puppy, he miserably fails after finding out the puppy had grown into a much bigger dog. Medaka helps him out, only for Shiranui to find out that while Medaka loves animals, animals don’t love her for some reason, with the dog fleeing from her and hiding behind Zenkichi.

Zenkichi has been going round to all the clubs for their trial period even though he’s already a Student Council member, earning him the nickname “Club Crasher”. After dealing with a small-time group trying to rebel against Medaka, the Student Council gets a request from the judo club to help them pick a new captain, where Zenkichi and Medaka see a familiar face: the “Prince of Judo”, Akune Kouki.

Zenkichi and Akune begin their match, and Akune quickly gains the advantage with 9 points out of a required 10, while Zenkichi hasn’t managed to get his required 1 point yet. Once Medaka encourages him, Zenkichi manages to win a point against Akune, and gets to stay in the Student Council. Because they can’t have a “prince” stronger than the new captain, Nekomi-senpai kicks Akune out of the judo club, and he goes to the student council, where he gets his first assignment – to help a senior write a love letter.

The Student Council realize they have a budget problem due to having no Treasurer, and decides to hold a competition in the rarely used swimming pool to decide which club will get extra funds. Boys are to be handicapped by giving them floats, with the first game being a water based version of ball-basket, in which clubs have to get 20 balls from the bottom of the pool and throw them into the corresponding basket.

The Swim Meet continues, with the second battle being a three-legged race for one length of the pool. The track team and Student Council finish 2nd and 3rd respectively, with the swim team finishing 1st due to having swum the entire length in sync. Shiranui announces the final battle to be a cavalry battle in the pool, specifically set up to pit the Student Council against the swim team; Medaka’s ideals clashing with Kikaijima’s.

Zenkichi walks down the hallways of the Academy, thinking to himself about the Student Council’s new Treasurer, Kikaijima. Though he thinks that this should be a good thing, with the budget now finally in order, he feels as though all the people who came after him have better positions then he does. He remembers Medaka telling him to work his way up, but it still doesn’t sit right with him. He then enters the Council’s room, to find a changing Kikaijima in her underwear. When Kikaijima demands that he pay for the show he got, Zenkichi is incredulous that she wants him to pay her money after already beating him up. He angrily tells her she was at fault for changing in a unisex room without locking the door, and that he should be asking her for money, as she showed him something he didn’t want to see. Kikaijima starts crying, and angrily cries that he pay her while calling him a meanie, now telling him to pay for the mean things he said as well. Zenkichi relents, and he pays her $4.50 for the peep show, and $3.00 for being mean. With Kikaijima’s mood improved, he thinks to himself that it was cheaper than he expected. Kikaijima asks him where the computer is, to which he replies that they don’t have one and hands her an abacus, much to her surprise. Zenkichi goes on to say that they don’t need a computer with Medaka, as she can do any kind of arithmetic in her head, to which Kikaijima questions whether Medaka has intel inside. She then claims that it is a waste to buy something that isn’t needed, and that an abacus is also pretty useful. Kikaijima begins working while Zenkichi starts reading manga.

Onigase is chastising Kanoya, Yatsushiro, Moji, and members of the Kendo Club for their improper clothing, refusing to let them into the school building. Moji and his friends brush her off, much to her ire. Yatsushiro goes on to point out the Student Council, whose flagrant disregard for the school’s dress code horrifies Onigase. She confronts the Student Council in their office, calling out all of the members on the problems with their uniforms: Zenkichi on wearing his jersey under his jacket (to which he admits he was trying to get others to copy him) and Akune on wearing his uniform in a manner akin to Elvis Presley (he remarks that he can’t retaliate if she gets angry like that). After Onigase calls out Zenkichi and Akune on their uniforms, she turns to Kikaijima. While Kikaijima initially denies having made an alterations to her uniform, Onigase successfully reveals that she has been wearing her swimsuit beneath her uniform. Zenkichi wonders if Onigase has x-ray vision, while Akune can only wonder why Kikaijima was wearing her swimsuit. An embarrassed Kikaijima tries to claim she was testing Onigase, prompting Zenkichi to ask her why she is trying to act high and mighty now.

Medaka heads to the music room to solve a complaint about the school orchestra being too loud while the other members deal with other suggestion box requests. Accompained by Onigase and Shiranui, she finds that the situation has already been dealt with by DisCom chairman Unzen Myouri, an abnormal known as the ”Monster Child”. Unzen declares his desire to fight against the Student Council and has sent 3 people to deal with Zenkichi, Akune and Kikaijima, and Medaka only has 3 minutes remaining to save them.

Medaka and Unzen's battle continues. When Unzen almost kills her friends, Medaka transforms into her "forte #4," War God, losing all control and giving into her rage.

Medaka continues to fight Unzen, gaining the upper hand until she is caught by his reinforced invisible wire and is unable to move, leading Unzen to think he has won. Medaka ends up moving the entire school building in an attempt to continue fighting, though Unzen says that because no reform has taken place, she should consider it her defeat. Just as she is about to deal a final blow, the rest of the Student Council members restrain her and she switches out of War God mode immediately, thanking Unzen and leaving.

After Medaka goes to the hospital to treat the injuries she received from fighting Unzen, the Student Council receive a request to find a missing shougi piece from a 2nd year, Mochibaru Sasae. After searching the room and finding no trace of the piece, Akune suggests that they ask Natayama, an ex-member that has a resentment towards the club.