Michael discovers that Madeline had Nikita "adjusted" in order to eliminate her emotions and keep her under strict control. Fearing this process will be used on everyone in Section One, Michael attempts to find the man who created this brainwashing.
Nikita and Michael pose as heroin dealers to get close to a dashing, drug-using playboy and arms supplier with ties to Red Cell. When the weapons dealer proposes marriage to Nikita, Operations orders her to accept.
Nikita's new husband, Helmut, reveals that he is an Interpol agent. Kristoff, Helmut's younger brother, hires Red Cell to kill his newlywed sibling, but Section One kills Kristoff. After disobeying an Interpol directive, Helmut becomes a man on the run.
Operations sends Nikita and Michael on a personal mission to help Operations' hero-Willie Kane, a fellow Vietnam War veteran. Walter kills Willie to prevent Operations from learning the truth about his hero...
Chosen for a pilot program allowing her to leave Section One but have no contact with either her former or Section lives, Nikita wonders if she's about to be cancelled. George orders Nikita to kill Operations, who supposedly killed her father.
George sends a two-man bio-tech team into Section One when a mysterious gas enters the headquarters, causing symptoms of a viral infection. Rather than contain the virus, the bio-tech team performs neural scrapes on the Section's top members.
When another Section gets destroyed, Operations sends Nikita and Michael to train a group of hostile, young recruits. Operations uses the team of recruits as bait to destroy a new terrorist group, Crystal Sky, and capture its leader.
Madeline falls in love with Leon, her Red Cell counterpart. Operations orders Madeline to kill Leon, but she shoots Operations instead. A tracking device implanted in Madeline leads Section One operatives to Leon's headquarters, where Operations kills him.
Michael discovers that his wife, Elena, is involved with a Section operative named Corliss. Stefan Vacek, Elena's uncle, heads a terrorist organization that tries to kill Elena and her son by Michael, Adam.
Birkoff uncovers the secret location of Red Cell's base camp, which harbors the leader of Red Cell--for whom Section has been searching for almost 20 years. When the mission to extract the Cardinal goes awry, Operations decides to kill Birkoff.
On his computer, Birkoff invents a form of artificial intelligence intended to maintain the system during his upcoming two-month vacation. The computer program develops an agenda of its own and kills Section operatives.
Section and Red Cell form an uneasy alliance to discover who's been destroying their installations. Madeline trades places with Satin Tate, a key Red Cell operative. Nikita worries about Satin's flirtatious behavior around Michael.
A new Red Cell regime surfaces, and Operations sends Michael and his team to assassinate Maurice Grenet, the Cardinal's replacement. Nikita escapes Section One, and Michael discovers her connection to Section One's foremost enemy.
Facial prosthetics makes Nikita look like Kate Quinn. Michael and Nikita/Quinn escape from Section One, killing Davenport in the process. Operations orders Madeline to capture them or lose her position.
Section One captures Nikita and Michael and brings them back to headquarters. Operations and Madeline decide to kill Nikita. Mr. Jones wants Madeline cancelled, but she commits suicide by ingesting cyanide.