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.
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.
A disgruntled operative, Kronen, shoots Operations and nearly kills him. Egran Petrosian, Operations' temporary replacement, wants Nikita as his second-in-command. Nikita accepts the promotion, but neither Nikita nor Michael trusts Petrosian.
Michael's mission to kill Dorian Enquist, a fringe member of the terrorist community, goes awry, and Enquist holds Madeline hostage. 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. 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 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 flee the country.
A surgeon paid by Red Cell implants a powerful time bomb in the abdomen of a human. Nikita intentionally gets arrested for smuggling hashish to make contact with Jenna Vogler, the only person who can identify the human time bomb.
Faced with too many missions and too few team leaders, Operations and Michael appoint Nikita as a team leader. Assigned to capture Phillip Stark, who has been buying spent fuel rods from nuclear reactors in Eastern Europe, Nikita chooses her own team.
Terry, a veteran operative who is pregnant, escapes from Section One in order to save her baby, but Nikita and Michael return her to Section One, not reporting the incident to Operations, to save Terry's life.
Section One steals secret files belonging to Orlando Perez, a high-level enemy operative from Red Cell, but Red Cell captures Michael and gets interrogated. An intravenous drug administered by Red Cell causes Michael to lose his memory.
A psychotic murderer and sadistic wife-beater who was thought to have been killed by Section One, David Fanning comes to work for Section because he knows its next target, Nikolai Kusko, the former head of the Romanian Secret Police.
An unknown terrorist group performs small bombings while preparing for a major act of mass destruction. In order to expose the terrorist group, Section One must figure out the computer code the group is using.
After seeing a bus depot filled with people get blown up by the terrorist group Bright Star, Nikita vows to stop its activities. Gregory Formitz, who supplies the group with forged passports, visas and press credentials, agrees to help Section One.
Section One uncovers a possible Red Cell munitions outpost in Glasgow, Scotland, and sends a team of operatives to overtake and neutralize the facility. Instead, Mowen returns to Section One bringing a deadly virus back with him.
With his massive financial resources, Abel Goellner destabilizes Third World countries friendly to the West and places hostile governments in control. Posing as money brokers, Michael and Nikita meet with Goellner and his confidante, Karel Giraldi.
Under Adrian's direction, Nikita risks her own life to retrieve incriminating files from restricted areas within Section One for Adrian's quest to destroy it. Operations and Madeline suspect that Nikita may be guilty of security breaches at the Section.