With Michael's help, Nikita survives Section One's assassination attempt on her, but Section One believes that she is dead. While working as a waitress, Nikita is kidnapped by the Freedom League and taken to the terrorist group's headquarters. Masquerading as a terrorist, Nikita saves Michael's life, and Michael and Nikita consummate their love. Nikita's brief period of freedom reveals to her that there is only one place she can live--Section One.

Nikita's deception could be uncovered when she must retrain with Jurgen, a special operations agent ordered to evaluate her physical, psychological and emotional states. Section One's capture of a high-ranking member of the Freedom League further imperils Nikita. Jurgen realizes Nikita is not telling the truth, but he does not report her to Madeline and Operations.

Nikita continues her retraining sessions with Jurgen, and Michael is not happy about it. Jurgen believes that Michael wants to kill him, and the two men fight. Nikita and Jurgen have affection for each other. Operations returns Nikita to full status.

Nikita visits Jurgen at his spacious country house. Nikita and Jurgen are about to make love when both are summoned for an assignment. Jurgen is blackmailing Section One. Jurgen volunteers for a suicide mission and dies. Operations promotes Nikita to class two operative--a position with more autonomy and responsibility.

A disgruntled operative, Kronen, shoots Operations and nearly kills him. Egran Petrosian, Operations' temporary replacement, wants Nikita--not Madeline--as his second-in-command. Nikita accepts the promotion, but neither Nikita nor Michael trusts Petrosian. Section One must destroy a nerve gas factory. Nikita proves that Petrosian manipulated Kronen into shooting Operations.

Michael's mission to kill Dorian Enquist, a fringe member of the terrorist community, goes awry, and Enquist holds Madeline hostage. Operations decides to trade Michael's life for Madeline's, and Nikita realizes that the only way to save Michael is to rescue Madeline.

Michael helps a college friend, Rene Dion, who heads a terrorist group, L'heure Sanguine, of which Michael was once a member. Rene took care of Michael's sister after Section One orchestrated Michael's arrest and phony "death," and now Michael repays the favor by helping Rene escape from Section One. Section One kills every member of L'heure Sanguine except Rene, who points a gun at Michael. Nikita shoots Rene and saves Michael.

Section One must stop Radovan Luca, whose contacts to the international arms community aid a rebel force inside the Balkans. While on a mission to eliminate the Balkan terrorist, Nikita and Michael help two children, whose parents were abducted by the rebel soldiers, flee the country. Birkoff discovers that his operative girlfriend is stealing money from terrorist accounts monitored by the Section.

A surgeon paid by Red Cell implants a powerful time bomb in the abdomen of a human, and Section One must find the carrier and identify the target. Nikita intentionally gets arrested for smuggling hashish to make contact with Jenna Vogler, an incarcerated Red Cell foot soldier and the only person who can identify the human time bomb. Walter flirts with an operative who is about to be placed in abeyance, but Birkoff changes her status.