"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 centers on Twilight, a highly skilled spy from Westalis tasked with a critical mission: to prevent war by infiltrating Ostania and gathering intelligence on Donovan Desmond, a powerful political figure. To achieve this, Twilight must get close to Desmond by enrolling in the prestigious Eden Academy, which Desmond’s son attends. However, gaining access to the academy requires Twilight to pose as a family man, as only parents of students are allowed to attend school events.

Twilight adopts the alias Loid Forger and hastily assembles a makeshift family to maintain his cover. He adopts Anya, a young girl with telepathic abilities, from an orphanage, and marries Yor Briar, an unassuming office worker who secretly works as an assassin. Despite their unconventional backgrounds, the three form a family unit, each hiding their true identities from one another. Anya, aware of her parents’ secrets through her telepathy, strives to keep the family together, fearing the consequences if their deceptions are revealed.

The narrative explores the dynamics of this fabricated family as they navigate their dual lives. Loid balances his spy missions with his role as a father, Yor struggles to reconcile her assassin duties with her newfound domestic responsibilities, and Anya attempts to excel at Eden Academy to help Loid’s mission while coping with her own insecurities. The series blends espionage, comedy, and heartfelt moments as the characters grow closer, blurring the lines between their fabricated roles and genuine emotions.

Key supporting characters include Franky Franklin, Loid’s informant and friend; Damian Desmond, Donovan’s son and Anya’s classmate; and Bond, a genetically enhanced dog with precognitive abilities who becomes part of the Forger family. The story progresses through episodic missions and school-related challenges, with overarching stakes tied to Loid’s mission and the fragile peace between Westalis and Ostania. The interplay of action, humor, and emotional depth makes "Spy×Family" a compelling exploration of family, identity, and the lengths people go to protect those they care about.