"SPY×FAMILY" is set in a fictional world resembling Cold War-era Europe, where tensions between the nations of Westalis and Ostania are high. The story revolves around a makeshift family formed for espionage purposes, blending action, comedy, and heartfelt moments. Twilight, a highly skilled spy from Westalis, is tasked with a critical mission: infiltrating Ostania's elite social circles to prevent a potential war. To achieve this, he must get close to Donovan Desmond, a reclusive politician who rarely appears in public. The mission requires Twilight to create a fake family, as Desmond only interacts with individuals who have families.

Twilight adopts a young girl named Anya, an orphan with telepathic abilities, to act as his daughter. Unbeknownst to him, Anya is aware of his true identity as a spy and is eager to play her part, hoping to maintain the stability of her new family. To complete the facade, Twilight recruits Yor Briar, a seemingly unassuming office worker who is secretly an assassin. Yor agrees to marry Twilight to avoid suspicion about her own double life. Together, the three form a family, each hiding their true identities from one another while navigating the challenges of their respective roles.

The narrative explores their daily lives as they balance their secret professions with the demands of family life. Anya enrolls in Eden Academy, an elite school where she must excel to help Twilight get closer to Donovan Desmond's son, Damian. Yor struggles to adapt to her new role as a wife and mother while continuing her work as an assassin. Twilight, though initially focused solely on his mission, gradually becomes emotionally invested in his makeshift family, creating a dynamic interplay between duty and personal attachment.

The series combines espionage, humor, and slice-of-life elements, with each character's hidden talents and vulnerabilities adding depth to the story. Anya's telepathy often leads to comedic misunderstandings, while Yor's lack of domestic skills contrasts with her deadly precision as an assassin. Twilight's meticulous planning is frequently challenged by the unpredictability of his new family. As the story progresses, the bonds between the characters grow stronger, even as they face external threats and the complexities of their intertwined lives. The series maintains a balance between lighthearted moments and the underlying tension of their high-stakes missions, creating a compelling narrative that appeals to a wide audience.