Section One's computer security is breached and the directory of all their agents is stolen. Michael goes to Prague to reclaim the directory, but the man who stole it is killed by another terrorist seeking the directory for himself. Nikita discovers that it was randomly left with a civilian passenger on a Prague city bus, architect Gray Wellman. Nikita is assigned to Gray in order to get close to him and retrieve the directory, but when she starts falling for him, her actions not only threaten the mission, but Section One's very existence.

The CIA believes that a rogue element of their agency is responsible for a recent massacre of heroin dealers, performed in order to steal money and drugs as part of an embezzlement scheme. Section One is brought in to clean the house quietly, but Nikita's continued involvement with architect Gray Wellman is tampering her ability to be a reliable operative. As Section One's operation reaches a fever pitch, Nikita is unable to balance both sides of her life, and is forced to make a choice between the organization that controls her life and the one man that she's ever loved.