"Yagami-kun's Family Affairs" centers on the life of Yagami Taichi, a high school student who finds himself entangled in the chaotic dynamics of his eccentric family. The Yagami household is far from ordinary, with each member possessing unique quirks and abilities that often lead to humorous and unpredictable situations. Taichi, the protagonist, is a relatively grounded individual who struggles to maintain a semblance of normalcy amidst the chaos. His father, Yagami Ryuichi, is a former spy with a penchant for over-the-top antics, while his mother, Yagami Akane, is a brilliant scientist whose experiments frequently go awry. Taichi's younger sister, Yagami Yui, is a prodigious martial artist with a fiery temper, and his older brother, Yagami Haruto, is a charming yet lazy college student who often avoids responsibility.

The narrative unfolds through a series of episodic adventures, blending comedy, action, and family drama. Each episode typically revolves around a new challenge or misadventure, often triggered by the family's unconventional behavior or external forces. For instance, Ryuichi's past as a spy occasionally resurfaces, leading to encounters with former allies or enemies, while Akane's experiments frequently result in bizarre inventions that disrupt the household. Yui's martial arts prowess often comes into play during conflicts, and Haruto's laid-back attitude contrasts sharply with the rest of the family's high-energy personalities.

Despite the constant chaos, the series emphasizes the importance of family bonds and mutual support. Taichi, though frequently exasperated by his relatives, ultimately steps up to protect and guide them through their various escapades. The interactions between the family members are marked by a mix of affection, rivalry, and comedic misunderstandings, creating a dynamic and engaging narrative. The show balances its comedic elements with moments of heartfelt sincerity, highlighting the Yagami family's resilience and love for one another, even in the face of their many eccentricities.