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.

The Penguin Spirit appears again and tells Shōma and Kamba to board a train and find a girl named Ringo Oginome who may possess the Penguindrum. With Ringo attending a girl's school, Shōma and Kamba send in their penguins to follow her. The brothers end up following her to a lingerie store, where they spot her maneuvering round the outside of a building in order to take a photo of something, which she shows to the brother's teacher, Mr. Tabuki. She then follows him home and hides out under his house, where the brothers conclude that she is a stalker, and pulls out a diary which allegedly fortells destined events.

As Ringo contemplates making a special curry for Tabuki, Shōma and Kamba, having been reminded about Himari's fate if they don't cooperate, break into Ringo's house to search for the Penguindrum. After just managing to hide from her when she comes back home to prepare her curry, the brothers follow Ringo to Tabuki's house, where she finds another woman living with him. Ringo swaps the curry she was preparing with her own and runs off, where she runs into Himari who invites her to her house, much to the brothers' surprise. After eating together, Ringo returns home and confirms the events laid out in her diary.

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.

Asami Kuho, the girl who was pushed down the escalator, is questioned by a woman named Natsume, who then fires a red ball at her head, causing her to remember nothing about the incident. Kamba hears that his uncle is planning to sell their house and goes to see a strange person to obtain the money to buy it. Meanwhile, Shōma and Himari find Ringo, who had a bad day, and invite her back to their place. There, Shōma asks Ringo about her diary, which she claims is a Diary of Fate which describes her future. Both she and Shōma are summoned by the Penguin Hat, who orders Shōma to retrieve the diary, but Ringo breaks free and throws away the hat which lands on a truck, causing Himari to fall dead again. As Kamba goes to retrieve the hat, he recalls what happened 9 years ago when he went with his father into a typhoon when Himari was ill with a fever. After a tough struggle, Kamba manages to retrieve the hat and return it to Himari.