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.

During a mission to destroy a Russian chemical plant, Michael is injured and is left behind. Section determines that it is too risky to save Michael, but eventually does go to find him by sending Nikita and Madeline in as travelling cosmetic saleswomen. Meanwhile, Michael kidnaps a nurse, Angie Georgiev and convinces her to help him before the head of the secret police, Egran Petrosian, is able to find him. Madeline and Nikita are able to determine where Michael could possibly be and arrive at Angie's apartment shortly after Petrosian does and extract Michael and Angie with Petrosian in pursuit. The four arrive at an abandoned airstrip to await air transport from Section when Petrosian's forces arrive, killing Angie in the fighting that ensued. It is later revealed that Petrosian is really a Section operative that has been in deep cover for the past 17 years. The ""rescue mission"" was really means to extract Petrosian from deep cover and bring him back into Section's fold.

Section captures a mathematician in order to decode a code that is aiding terrorists in their attacks.

Section falls into a trap when a mission to take out a Red Cell munitions base causes a virus to be spread throughout Section.