Act I
Florestan, a Spanish nobleman who challenged the authority of the governor Pizarro, has been imprisoned by him. Although it is widely believed that Florestan is dead, Leonore, his wife, is convinced he is still alive. Under the name of "Fidelio" and dressed as a young man, she has for two years been working as helper to Rocco, the jailer of the prison. Rocco's daughter Marzelline has fallen in love with Fidelio, to the dismay of Fidelio and the grief of Jacquino, Rocco's gate-keeper.

As the action begins, Jacquino professes his love and jealousy to Marzelline, who in turn speaks of her love for Fidelio. Rocco and Fidelio enter and the four sing of their individual thoughts and feelings. Rocco agrees to the marriage between Fidelio and his daughter. Fidelio begs Rocco to be allowed to help care for the political prisoner who is kept in the subterranean cell of the prison and who she suspects may be Florestan. Rocco reports that the man is wasting away, but that he will ask permission for Fidelio to accompany him.

Pizarro arrives with his soldiers and learns from a dispatch that Fernando, the minister of state, is coming to inspect the prison, having heard that Pizarro is misusing his power and unjustly imprisoning personal enemies. Pizarro realizes that Florestan must be permanently removed. After stationing a trumpeter in the tower to give warning of the minister's arrival, he charges Rocco with the job of preparing Florestan's grave and helping in the removal of the "enemy of the state." When Rocco refuses to commit the murder, Pizarro decides to do it himself. Leonore has overheard the conversation and, when alone, expresses her fury and determination to free Florestan. She persuades Rocco to allow the prisoners into the prison courtyard, but when they stumble blindly out into the light she is disappointed not to see Florestan among them. Pizarro enters in anger, ordering the prisoners back to their cells.

Act II
Scene 1. In his dark dungeon, Florestan dreams of Leonore, whom he imagines coming to free him. But his vision turns to despair and he sinks down exhausted. Rocco and Fidelio enter and set about digging the grave. Florestan does not recognize Leonore, but when he asks Rocco the name of the governor of the prison, Leonore recognizes her husband's voice. At a signal from Rocco, Pizarro enters and reveals his identity to Florestan, announcing his intention of killing him. But just as he is about to do so, Leonore rushes between them with a pistol. At that very moment the trumpet sounds, announcing the minister's arrival. Pizarro has no alternative but to depart to greet Fernando, and Leonore and Florestan exult in their reunion.

Scene 2. Pizzaro's reign of terror is over. In the prison courtyard Fernando proclaims justice for all and releases the prisoners, while Leonore herself removes Florestan's chains. All join in a jubilant closing chorus.