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The pilot begins with the announcement of the 98th student body president: freshman Class 13's Medaka Kurokami. Medaka comes forward to make her inaugural speech, and declares that she is establishing a suggestion box. After the opening ceremony, Shiranui chases down Zenkichi, expressing her surprise that a freshman got elected president. Zenkichi claims he is not surprised, as nothing Medaka does surprises him anymore. Shiranui asks him if he is going to join the Student Council, which Zenkichi vehemently denies. At the moment, an announcement is made on the loud speaker, asking Zenkichi to report to the Student Council room. Zenkichi angrily stomps off, insisting that he helped Medaka with the election because she told him it would be "just this once", as Shiranui laughs. Another girl asks Shiranui what the relationship between Zenkichi and Medaka is. Shiranui calls them childhood friends, who have grown apart.
Zenkichi enters to Student Council room to find Medaka in her underwear. He immediately shuts the door, only for Medaka to open it (still undressed) and tell him to come in. She then asks him why he is so embarrassed about seeing her naked, as the two of them took baths together as children. Zenkichi claims he remembers nothing of the sort, and asks when the Student Council uniform became so embarrassing. Medaka claims she has no problem showing off her body. Zenkichi also notes that she is wearing the armbands of all members of the Student Council; Medaka states she is currently fulfilling all roles until she can find more members. Zenkichi thinks to himself how there is nothing Medaka can't do, and asks out loud what she wants of him. Medaka asks him to help her with the suggestion box, and though Zenkichi initially refuses, after a pleading look form Medaka, he agrees to "just this once". He then remembers how, since they were children, he has always been dragged around by Medaka. As Zenkichi sorts through the suggestion box, he finds one request that looks serious.
At the Judo Club, Akasaka talks to the captain. The captain tells him that he left a request in the suggestion box asking for the Student Council's help: because the club has only four members, they can't compete in the customary competition with their sister schools. If they lose, their club will be disbanded. Akasaka is horrified, as their club is in no danger, and the competition is just a friendly match. The captain says that the exaggeration is fine, and that they will borrow Zenkichi for the competition. Akasaka shows his worry, claiming that though he has never spoken with Zenkichi, he hasn't heard very good things about him. As the four members leave the changing room, they find Medaka and Zenkichi (both in judo uniforms) waiting for them. Medaka immediately orders all five boys into the seating position, and then tells the club members that, because they don't have enough people to participate, she will lend them Zenkichi. However, she goes on to say that such a method won't help them in the long run, and that the club will need to be reformed, to the point that they will be capable of winning in the gold medal in Judo at the next Olympics. There is an immediate outcry from the club, with the captain insisting that there small group, even if they were larger, have no way of doing something like that. As Medaka tries to convince the club otherwise, Zenkichi thinks to himself that things are going just as he expected. He remembers how in middle school, Medaka simply told runners to run faster if they wanted to win races; she has no concept of what it's like to suffer or lose. Medaka proclaims that she will train with the Judo Club, and orders Zenkichi to come and spar with her. The club members are then stunned when Medaka easily flips Zenkichi, and are then horrified when he reveals that Medaka has a Red Obi. The club tries to talk their way out of training, but Medaka insists that she will come every day to work with them, and then tells them to get ready. On the floor, Zenkichi mentally gives them his condolences.
Two hours later, Shiranui shows up at the club, only to find all of the members (and Zenkichi) beaten black and blue. Shiranui tells Zenkichi it is pointless to try and improve the Judo Club, much to Akasaka's ire. Shiranui tells him to shut up, and then tells Zenkichi to pass on a message to Medaka for her: "It's pointless to force people to do their best if they don't want to. Or something like that." Shiranui then leaves, and Zenkichi thinks to himself that she is full of herself, though he doesn't understand her words until the next morning.
When Zenkichi and Medaka come to club, they find Akasaka by himself and out of uniform, with letters of resignations from the members of the Judo Club; the seniors do not think they will be able to meet Medaka's demands. Medaka notes that there are four letters, and asks Akasaka if he intends to quit as well. Akasaka angrily tells her that all he wanted was to practice Judo, but that it is pointless if he is the club's only member, and storms off. Zenkichi is surprised, thinking of how angry Akasaka was made by Shiranui's words the previous day. Medaka then tells him that the two of them will begin morning practice, causing Zenkichi to ask her if she even remembers why they started coming in the first place.
At lunch, Shiranui tells Zenkichi that the Judo Club used to be pretty strong, but that the current captain favors "fun Judo" over "excellent Judo", an attitude that lead the club to becoming a haven for lazy practitioners. Disgusted, all the serious practitioners left, leaving the club with only four members. Shiranui goes on to tell Zenkichi that the captain lied about the club being disbanded if they lost the competition; even if it was true, there isn't a single person in the school who would care.
Walking by himself, Akasaka remembers how all the other members told him it was a mistake to get involved with Medaka. The captain apologized for how things turned out, and then handed Akasaka his letter. Akasaka vents his frustration, and runs into Medaka who asks after him. He tells her to leave him alone, saying he has nothing to do with her anymore. Medaka tells him she can't do that, and that the competition is still on. Akasaka questions why Medaka and Zenkichi are doing so much for a bunch of strangers. Medaka tells him that is a stupid question, as her raison d'etre is helping others, and that she only feels happy when she does so. She then goes on to ask Akasaka if he is really happy with the way things are. Akasaka angrily tells her that not everyone is as strong-willed as she is and runs off. Medaka says to herself that just because she is strong, it doesn't mean others are weak.
At the Judo Club building, Medaka announces the start of the competition between Hakoniwa Academy and Suisou Academy. Zenkichi stands alone before five others; the opposing team is understandably upset by this. However, Beppu from the opposing side says that it isn't a problem, and declares if the Student Council President and her childhood friend want a public lynching, he will give them one. Medaka tells Zenkichi not to worry and that it isn't his job to win; Zenkichi replies that he is only helping her out this once. Akasaka thinks to himself that it is almost time for the competition, but then remembers he is no longer a member of the club. Shiranui calls out to him, and despite his protests, drags him with her to the Judo Club, telling him that "everyone" is going to see it. From the window, Akasaka finds the other members, and looks on to see Zenkichi getting beaten by Beppu. The captain states that Zenkichi is doing his best, but that his opponent is too strong. Another member states that Beppu nearly killed all his rivals from middle school, and that he is deliberately drawing out the match so that he can continue to beat Zenkichi. Beppu and Zenkichi exchange barbs, and outside, Akasaka asks the captain if they are enjoying themselves right now. The captain answers that of course they aren't, and Shiranui shows up behind them, telling them things aren't always as simple as enjoying yourself, and that they should move so she can get a better view. Inside, Beppu drops Zenkichi on his head. Thinking the match over, he asks Medaka if she is next. She tells him not to make light of her childhood friend, as Zenkichi rises to his feet. Beppu demands to know why Zenkichi is pushing himself so hard when he isn't even a member of the Judo Club. Medaka tells all assembled that it is because Zenkichi has been in love with her since he was two, and that it is normal to your best for the ones you care about. As the Judo Club members burst in, Medaka tells Zenkichi he can win now. Zenkichi proceeds to drop Beppu, announcing that he has been practicing Judo since he was two, and then collapse from exhaustion. Outside, Shiranui sits in a tree, looking satisfied with herself.
Later, Medaka is seen bandaging Zenkichi. Out of four matches, the Judo Club won two and lost two, but they weren't satisfied with those results, and decided to do better at the next competition. Medaka talks about how she wanted to teach the Judo Club the importance of the words "to enjoy what one loves to do". She thinks her methods might have been a bit drastic, though Zenkichi notes that he was the only one that gotten beaten up. He then expresses his alarm when he sees Medaka has put the armband of the Vice-President on his arm. He insists that he was only helping her this once, and that she should be fine on her own. Medaka tells Zenkichi that she has nothing she loves, and that she can't do anything without him. She then pulls him into a hug, asking him to remain by her side. Zenkichi finally gives up, declaring "Only just this once!" The last image is of the suggestion box, with "meyasu" having been written over with "medaka".
Shiranui hosts a bonus panel, which depicts Medaka and Zenkichi showing up at the Judo Club for morning practice again, worrying the members as to whether she will really show up every day.
Characters in Order of Appearance
*Note: Bold = First Appearance
- Medaka Kurokami
- Zenkichi Hitoyoshi
- Hansode Shiranui
- Judo Club Captain (Pilot)
- Fat Judo Club Member
- Skinny Judo Club Member
Differences from Series Proper
- The Judo Club has only four members, none of whom are carried over to the actual series. Instead, the Kendo Club fulfills a similar role, while the Judo Club is completely different.
- Zenkichi is a Judo practitioner, as opposed to using Savate.
- Zenkichi becomes the Vice-President, as opposed to the General Affairs Manager.