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 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.

Kamba goes to see Asami only to find she has forgotten all about him. He tries getting some information out of two other girls, but they are attacked by Natsume's red balls, causing them to lose their memories. Meanwhile, Shoma reluctantly follows Ringo's orders in order to let her have her diary, having him move a lot of stuff over to Tabuki's apartment, but she ends up coming down with a fever. It is revealed that Ringo's late sister, Momoka, used to date Tabuki and Ringo felt that, in order to be accepted by her family, she would have to become Momoka by fulfilling what was written in her diary. Despite her fever, Ringo sneaks off to under Tabuki's house to spend her 'first night' with him, whilst Natsume is shown to have her own penguin, discussing 'Project M' with someone.

Tabuki invites Ringo to see one of Yuri's plays with him, followed by dinner, where Yuri invites her and Shoma to a party. At the party, Yuri announces that she and Tabuki are engaged, but Ringo remains determined, dragging Shoma to her school to help her make a love potion, which is foiled by Shoma's penguin. Determined to complete her mission, Ringo sneaks into Tabuki's room one night with the intention of getting impregnated by him.

Ringo attempts to make a move on Tabuki only to find he is not there as his roof had a leak. The next day, Tabuki tells Shoma that he is moving in with Yuri, which does not settle well with Ringo, who later discovers her father consorting with another family. Undeterred, she visits Tabuki's new apartment whilst Yuri is on tour, using a special cake to drug Tabuki whilst she pretends to be Yuri in order to have sex with him. However, Shoma manages to regain his consciousness and delay Ringo enough before Yuri returns home. As Shoma tries to stop Ringo from taking things any further, her diary is knocked off and is later ripped in half by a passing motorcyclist when she tries to retrieve it. As the shock leads Ringo to walk into the path of an oncoming car, Shoma manages to push her out of the way but is hit himself.

Himari has a strange dream in which she meets a man named Sanetoshi, who shows her various books containing her memories. In elementary school, she formed a group called Triple-H with her best friends, Hibari and Hikari. When she argued with her mother over buying a wrong ribbon, her mother became scarred from a falling mirror, she and her friends tried to kill a koi for its blood to heal her mother. She left elementary school due to her illness whilst her friends went on to become idols. Upon waking up after vaguely recollecting a soulmate she once had, Himari hears from Ringo about Shoma's accident.

Shoma wakes up in hospital with supposedly minor injuries, keeping quiet about what happened between him and Ringo from his siblings. As Ringo explains what happened to her diary to him, Natsume disguises herself as a nurse and kidnaps Shoma, demanding the other half of the diary from Kanba and Ringo in exchange for his life. Deciding the to leave the diary half with Ringo, Kanba goes to find Shoma, whilst Ringo is told to surrender the diary herself. After luring Kanba into a trap and kissing him, Natsume escapes but is confronted by another person in a penguin hat, whom Natsume identifies as Mario.

Kanba goes to confront Natsume about the memory-erasing balls and why she desires the diary, unaware that she only has half of it. Meanwhile, Ringo is still determined to complete Project M with or without the diary, making a love potion to give to Tabuki, which actually seems to work. As Ringo decides she can't go through with it, Yuri helps her come to the realisation that she is actually in love with Shoma. As Penguin Himari brings Shoma and Ringo into a Survival Strategy meeting, Himari tells them about the day 16 years ago when Momoka died and she was born, which turns out to be the day that Shoma and Kanba were also born.

Kanba goes home and is called by Sanetoshi claiming that Himari will die once more. Shoma goes into detail of what happened 16 years ago, as Shoma and Kanba's parents were high ranking members of a terrorist organization and were responsible for a terrible incident which killed Momoka. Himari still possessed loses her strength and tells Shoma and Ringo to acquire the Penguin Drum and to stop "them". Himari is then transferred to an hospital and Kanba is called by Shoma. He arrives to find Himari lying dead and tries to once more make a pact to give her his life, but it does not work as she says she must leave to "The Destination of Fate". Just as Himari seems to be truly dead, Sanetoshi appears.

Sanetoshi offers Kanba a special medicine to revive Himari, though mentions there will be a steep price in return. Kanba recalls three years ago when he and Shoma learned about their parents being criminals. Later, Sanetoshi contacts Natsume, who had also made a contract with him to save Mario, telling her who has the other half of Ringo's Diary. Meanwhile, Ringo talks to Tabuki, who helps put her worries to rest.

Yuri, after breaking off an affair with one of her co-stars, feels a longing for a certain someone. Meanwhile, Shoma is ignoring Ringo, feeling she will never be able to forgive him for what his parents did, and tells her they shouldn't see each other again. As Kanba tries to raise more money to pay for Himari's medicine, he is confronted by Natsume, who questions his feelings for Himari. As Ringo becomes depressed over what happened with Shoma, she is picked up by Yuri, who takes her to a hot spring inn and drugs her. It is revealed that she had a thing for Momoka and was the one who stole half of the diary that night, as she decides to act out her sexual desires on Ringo.

Yuri holds Ringo into her room that coincidentally is next to a room Shoma is staying with a classmate on a field trip. Shoma rushes to rescue her after figuring this but he trips and falls unconscious after bumping his head. Meanwhile, Yuri reminisces about her father, a famous artist who used to tell her she was ugly and convinced her to let him use his chisel on her as he claimed that by only making her "beautiful" he would be able to love her. Yuri started getting seriously injured by her father and she makes friends with her classmate Momoka who claims that her diary has the power of transferring fates in exchange for a price. Back to the present, Natsume appears before Yuri to steal the half of the diary in her posession and despite seemingly sucessful, it is revealed that she was tricked by Yuri and left with a forgery. After Shoma awakes, Yuri reveals to him that she has half of the diary and just like Momoka saved her from her abusing father by severely injuring herself with the power of the diary, Yuri is determined to use it to bring her back to life.

After realizing that she was tricked by Yuri, Masako reminisces about her grandfather, a powerful business tycoon who expelled her father claiming that he was not strong enough to be allowed a place in the Natsume family. After dreaming countless times about having him killed, Masako rejoiced when her grandfather inadvertedly poisoned himself to death by eating ill prepared Fugu. Masako since then assumed control of her family's corporation but was sad that her father had never returned home, until somehow her grandfather's spirit posessed Mario's body and forced her to eat the same poison that killed him to protect her brother, but Sanetoshi appears to save her life. Later, Masako sees Kanba hanging out with the same elusive men who took her father away and Sanetoshi asks Masako to join them in his plan to "put the world back on track" but she promptly refuses.

The Takakura siblings are enjoying Takoyaki together and happy with the news that Himari will soon be released from hospital when the magic hat posesses Himari again for another Survival Strategy meeting with her brothers and insists that their ordeal will not be over until the Penguin-Drum is retrieved. Meanwhile, Yuri and Tabuki reminisces about their childhood days with Momoka and while Yuri is unable to forgive the siblings for their parents' crime, Tabuki tries to dissuade her. In the next day, Himari leaves by herself with Ringo for shopping much to Kanba and Shouma's despair as they are informed that she must take another dose of her medicine before sunset. While the brothers look for Himari, Ringo receives a call from Yuri who invites her and Himari for a meeting. Yuri waits for Himari, but is intercepted by Masako instead, and the two start fighting for the two halves of the diary, while Himari and Ringo are approached by Tabuki who invites them to a construction site where he claims he will finally bring punishment to the Takakura family.

Tabuki reminisces about how he injured his own hands in despair of being relenquished by her mother as she only cared about his younger brother who was a much better pianist than him. After Tabuki traps Ringo at an elevator and holds Himari hostage, he phones Kanba demanding to bring his father to him. Kanba arrives alone to meet them, claiming he has no idea where his father is and finds Himari hung over into a construction bucket. Tabuki does not believe him and Ringo decides to call the police, but Kanba asks her to not do it and she calls Shouma instead. Tabuki reveals that Himari's brother is receiving money from his father's organization to pay for her treatment, and remembering about how Momoka had her hand severely injured to save him, Tabuki starts severing the wires holding the bucket one by one, claiming thet the only way for Kanba to prevent Himari from falling to her death is by sacrificing his own hand to hold the final wire together when it snaps. Kanba does so and despite his pain, he claims he would never have his sister die. Himari than decides to jump by herself to spare Kanba's life, but Tabuki saves her from the fall after seeing in Kanba the same determination to protect his sister he saw in Momoka when she saved him. Shoma arrives soon later and the siblings reunite in tears while Tabuki makes his leave, meeting Yuri on the way who reprimands him. It is also shown that Yuri's showdown with Masako ended in a draw, as each one still holds a half of the 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.

Masako decides to leave the Takakuras alone, still not accepting the 'family' they have. As Himari has another conversation with Sanetoshi, Shouma confesses to Ringo that Himari is not actually his blood sister. Years ago, whilst his parents were organising to change the world with their organization, Shouma met the orphaned Himari whilst exploring his condo. Whilst she is initially passive of him, the two grew a friendship over an abandoned kitten they find, up until it ended up being taken away. When Shouma discovered that Himari had headed over to the 'Child Broiler', where unneeded children go to disappear from the world, he rushed over there to rescue her and chose her to become a part of her family. Back in the present, Kamba continues to converse with his parents about what needs to be done to change the world.

Ringo is approached by a journalist asking about the Takakura siblings, but she avoids him and warns Himari about him. Later that night, Himari, who was told by the same journalist about how Kanba have been collecting money for her treatment, trails him to the shop where he supposedly meet his parents just to find the place torn down and have a shocking revelation. Shouma is informed by the journalist about Kanba's involvement with the Kiga Group and tries to stop him by force with no success. Meanwhile, Tabuki and Yuri also reach the shop and just like Himari, find the skeletons of the Takakura couple before being attacked by an unknown assailant. Shouma, who finds that Kanba ordered the journalist to be killed in a car accident, and was informed by Sanetoshi that the medicine will not prolong Himari's life for long, informs her that they can't live as a family anymore and sends her to live with his uncle. Later the Kiga group, whose true leader is actually Kanba prepares themselves to make a large scale operation, and Himari, seen standing next to him, claims that she is determined to stop him at the cost of her life.

Ringo stumbles on two girls dressed suspiciously standing before the Takakuras' house and finds that they are actually Himari's childhood friends Hibari and Hikari from the Double-H idol duo. They ask her to give Himari a present in return for the scarves she knit for them before leaving. Kanba learned from Sanetoshi that his medicine will not work on Himari anymore, and that according to him, she can only be saved after he fulfills his group's objective. Himari tries to dissuade him with no success and discovers that his hideout is situated under the aquarium where she first died. She prays for God to have Kanba saved in exchange for her life and falls lifeless on the ground. Yuri calls Ringo and returns her the half of the diary in her posession and stays beside an unconscious Tabuki at the hospital, who was stabbed by the attacker who was revealed to be Yuri's former lover and co-worker. Masako tries to convince Kanba to give up as the police is already aware of his plans and has a warrant on him, but he moves forward ignoring her pleas until they are surrounded and he puts himself im harm's way to protect her. Injured and unconscious, Kanba is carried away by his comrades while Masako decides to confront the police by herself to cover his escape.

On the day of the terrorist attack, 16 years before, Sanetoshi is contronted by Momoka who was determined to stop him and while her spirit ends up split in two with each half becoming the penguin hats used by Himari and Mario, his is divided into the two black rabbits that always accompany him. Back to the present, Shouma is informed that Himari's life is at its end and Ringo conforts him while Kanba is taken by Sanetoshi to a gravely injured Masako and brings her from the dead before his eyes. Despite Masako's pleas, Kanba leaves with Sanetoshi to continue his plan, carrying her half of the diary with himself. Shouma sees a vision of Himari asking him to stop Kanba, and when his brother comes to fetch her, he is shot unconsious by him with a penguin bullet. Ringo is called by Kanba to the aquarium and a bomb explodes knocking her out. Sanetoshi watches her struggling to stop her half of the diary from being burned out and after she fails, he has Kanba burn the other half. Shouma wakes up and manages to reach Kanba determined to stop his plans.

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.