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In a small Seoul neighborhood, Won Ryu-hwan (Kim Soo-hyun) appears to be a mentally challenged young man known for tripping on rocks, talking to himself, and generally being the village idiot. In reality, Ryu-hwan is a North Korean special-forces operative — one of the legendary 5446 Unit's most-skilled assassins — who has been embedded undercover in the neighborhood for two years awaiting reactivation orders.

Ryu-hwan's elite combat skills are hidden behind his bumbling village-idiot facade. The film's first act establishes his daily routine: helping local children, being mocked by neighborhood adults, secretly maintaining his physical training in private. His relationships with the neighborhood residents — particularly with a kind elderly woman and a young university student named Lee Hae-jin — provide emotional weight that contradicts his official mission.

Two more 5446 Unit operatives — Lee Hae-rang (Park Ki-woong) and Lee Hae-jin (Lee Hyun-woo) — are deployed to the same neighborhood with separate undercover identities. Hae-rang poses as a rock-band singer; Hae-jin (no relation to the university student) poses as a high-school student. The three operatives' shared mission becomes complicated when they must work together while maintaining their separate cover identities.

The political context shifts when the North Korean regime undergoes succession changes. The new leadership decides to eliminate all foreign operatives to avoid international incidents; an order goes out to the 5446 Unit operatives in South Korea: commit suicide within 24 hours. Ryu-hwan, Hae-rang, and Hae-jin receive their orders simultaneously. The franchise's primary moral conflict is whether to follow the suicide order or defect to South Korea.

Ryu-hwan refuses to commit suicide. His connection to the neighborhood — particularly to the elderly woman who has been kind to him — has made him incapable of leaving them. Hae-rang and Hae-jin similarly refuse. The three operatives become marked for elimination by North Korean assassins sent to enforce the suicide order; the film's third act becomes a sustained combat sequence as the three defend their adopted neighborhood.

North Korean assassin Kim Tae-won (Son Hyun-joo) arrives in the neighborhood to eliminate Ryu-hwan and his unit. Their confrontation features extensive practical-effects combat across multiple locations. Ryu-hwan ultimately defeats Kim but is mortally wounded; he dies in the elderly woman's arms, having protected his adopted neighborhood. The franchise's primary emotional catharsis is Ryu-hwan's death — a sacrifice that honors both his combat heritage and his adopted humanity.