"Penguindrum" centers on the lives of the Takakura siblings—Kanba, Shoma, and Himari—whose lives take a dramatic turn after a fateful visit to an aquarium. Himari, who suffers from a terminal illness, collapses during the outing and is pronounced dead shortly after. However, she is miraculously revived by a mysterious entity residing in a penguin-shaped hat purchased at the aquarium. This entity, known as the "Penguin Drum," grants Himari a second chance at life but imposes a condition: the brothers must locate the elusive "Penguindrum" to sustain her survival. Failure to do so will result in Himari's death.

As the brothers embark on their quest, they encounter a series of surreal and interconnected events involving a terrorist attack from years prior, a secretive organization, and a girl named Ringo Oginome, whose obsessive pursuit of a man named Tabuki intertwines with their mission. Ringo's actions, driven by a diary she believes holds the key to her destiny, complicate the brothers' efforts, as her goals often clash with their own. The narrative delves into themes of fate, memory, and the consequences of human desire, with each character's past gradually unraveling to reveal their connections to the central mystery.

The story is layered with symbolism and nonlinear storytelling, blending elements of psychological drama, dark fantasy, and social commentary. The penguin-shaped hat, which houses the entity controlling Himari's fate, becomes a recurring motif, as do the three small penguin companions that accompany the siblings, each representing aspects of their personalities and struggles. The series explores the moral ambiguities of the characters' choices, particularly Kanba and Shoma, as they grapple with their love for Himari and the lengths they are willing to go to save her.

Throughout the narrative, the concept of the "Penguindrum" remains enigmatic, serving as both a literal and metaphorical goal. The series builds toward a climactic revelation that ties together the disparate threads of the story, culminating in a resolution that underscores the cyclical nature of fate and the interconnectedness of the characters' lives. "Penguindrum" is a complex and thought-provoking series that challenges viewers to piece together its intricate narrative while exploring profound themes of sacrifice, identity, and the human condition.