Three siblings, Shōma, Kanba and Himari Takakura are living together, despite the fact Himari was given only a few months to live by the doctor. The three visit an aquarium to see the penguins, where Shōma buys her a queen penguin hat. However, Himari collapses and later dies in hospital. As the brothers mourn, they are surprised to see Himari suddenly spring back to life and cured of her condition, possessed by a spirit which has decided to extend her life, though she returns to normal when her penguin hat falls off. The next day, the siblings receive a shipment of frozen things, which are later revealed to be a trio of strange penguins that no one besides them can see. Just then, the hat possesses Himari again, explaining that she has extended her life but in exchange wants the brothers to obtain something known as the Penguin Drum. As Shōma sleeps that night, Kanba ends up kissing Himari as she sleeps.

As Ringo gets help from Himari preparing lunch for a 'date' with Tabuki at the park, Kamba tasks Shōma to go with her and look through her bag for her diary, believing it may be related to the Penguindrum. When they reach the park, they encounter a runaway skunk who runs off after squirting Ringo in stink. After changing clothes, Ringo and Shōma meet up with Tabuki, who brings along the woman Ringo saw him with, an actress named Yuri Tokikago. Come lunchtime, Ringo's prepared lunch gets eaten by crows, leaving her in the shadow of Yuri's picnic. In order to fulfil a 'first kiss' note in her diary, Ringo plans to jump into the pond and have Tabuki save her. However, the skunk appears again and knocks her in, forcing Shōma to save her instead and use CPR on her, though Ringo believes Tabuki to be the one who did it. Later that evening, a girl that Kamba met up with earlier is pushed down the escalator of a train station, completing the description in Ringo's diary.

After the incident at the construction site, Tabuki quit his job and leaves Yuri, while Kanba is praised by his parents for protecting Himari, claiming that once their true objective is reached, they will become together again. Kanba makes use of some money he got from them to throw a party for Himari with Shouma and Ringo to celebrate her return home, while Himari wonders about her conversation with Sanetoshi as she doubts that she will eventually be cured. He also has a conversation with Masako, who reaffirms her intentions to stop his plans. Masako then pays a visit to Himari and demands her to remember about her true past, as she claims Himari is not Kanba's real sister. She points a gun that in opposite to her usual memory-erasing bullets, contains memory-regaining ones, but is stopped by Kanba and Shouma who had just returned home. However Himari manages to remember her past and realize that her soulmate is actually Shouma.

Shouma tries to dissuade Kanba with no success while Ringo also boards the train, claiming she had learned from the present she got from Himari's friends the secret spell contained into the now lost diary. She activates the spell determined to sacrifice herself to save Himari and the others, but Shouma takes the burden to himself instead while Kanba sacrifices himself to ressurect Himari for good. The terrorist attack is stopped and both Himari and Ringo are found unconsious with no memories about the brothers or everything that happened. The same occurs for Masako whose brother Mario also fully recovers. While hanging with Ringo at her house, Himari finds a message left by Kanba and Shouma and starts crying without knowing the reason why while Shouma and Kanba, in children form, pass in front of her house accompanied by the four penguins.