"Kaichū!" centers around the life of a high school student named Nagisa Mikogami, who unexpectedly becomes the caretaker of a mysterious creature known as a "Kaichū." These creatures are small, sentient beings that resemble aquatic animals and possess unique abilities. Nagisa's Kaichū, named Kaito, is particularly unusual, as it exhibits traits and powers that set it apart from others of its kind. The story unfolds as Nagisa navigates the challenges of balancing her ordinary school life with the responsibilities of caring for Kaito, all while uncovering the secrets behind the Kaichū's origins.

The narrative delves into the growing bond between Nagisa and Kaito, exploring themes of trust, friendship, and the complexities of coexistence between humans and otherworldly beings. As Nagisa learns more about Kaito's abilities, she becomes entangled in a series of events involving other Kaichū caretakers, each with their own motivations and struggles. The series introduces a diverse cast of characters, including rival caretakers, scientists researching the Kaichū phenomenon, and individuals with hidden agendas. These interactions drive the plot forward, revealing the broader implications of the Kaichū's existence and their impact on the world.

Throughout the series, Nagisa faces moral dilemmas and personal growth as she grapples with the ethical implications of her role as a caretaker. The story also examines the societal reactions to the Kaichū, ranging from fascination and acceptance to fear and exploitation. As the stakes escalate, Nagisa and Kaito must confront external threats and internal conflicts, culminating in a climactic resolution that ties together the various narrative threads. The series balances moments of lighthearted humor and heartfelt emotion with action-packed sequences and thought-provoking themes, creating a multifaceted viewing experience.