The Secret Agent is set in Brazil in 1977, when the country was under military dictatorship, described as a ‘period of great mischief’ by the film’s intertitle. Marcelo (Wagner Moura), a widower who is on the lam, arrives in his hometown, Recife, to reunite with his son Fernando (Enzo Nunes), who lives with his late wife’s parents. Marcelo is provided refuge by the kind and spirited Dona Sebastiana (Tania Maria), who harbours a couple of other political refugees in her building. The fugitives celebrate the Carnival exuberantly, though their lives are under threat by the dictatorship.

Ironically, living under a fake alias, Marcelo (whose real name is Armando), gets a job at a state identification office, and makes it his mission to find his late mother’s ID card in the archives. As the film unfolds, we learn why Marcelo, despite not exactly being a dissident, insurrectionist or even a secret agent, as the title suggests, finds it necessary to flee the country. The film is divided into three parts, and fragments of Marcelo's life under the military dictatorship are reconstructed by two college students in the present, through audio recordings made by the resistance group.