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 mysterious Gelman, the man who created this form of brainwashing. Operations learns of Michael's search and gives the order to have Michael cancelled.

Madeline intructs Nikita to carry out Operation's order to kill the missing Michael. Nikita has a physical confrontation with Michael when he infiltrates Section One, and she ends up bound and gagged. Michael kidnaps the cryogenically preserved Adrian from Section One, and Birkoff pretends not to see the rogue operative's activities.

Determined to reverse the effects of Gelman's mind-control process on Nikita, Michael enlists Adrian's aid. Operations and Madeline send Nikita to kill Michael, but he kidnaps her instead. Michael thwarts Operations and Madeline's plan to kill George from Oversight. Michael regains his former status within the Section.

Nikita continues to suffer the negative effects of Gelman's brain reprogramming, which becomes permanent in five days. With Birkoff and Walter's support, Michael kidnaps Nikita to deprogram her. After being restored to her former self, Nikita returns to Section One, where she lies to Madeline about her true feelings for Michael.

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, but Operations thinks Willie's murder is a Mob hit and wreaks a staggeringly harsh vengeance. Birkoff discovers he has a twin brother.

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 years ago. Madeline tells Nikita that Operations is really her father, but he will not answer any of Nikita's questions. George reveals the dead body of a look-alike, but which one gave Nikita the order to kill Operations?

George sends a two-man bio-tech team into Section One when a mysterious gas enters the headquarters, causing symptoms of a viral infection in several people. Rather than contain the virus, the bio-tech team performs neural scrapes on the Section's top members, totally incapacitating Walter and Nikita. Michael injects George with a syringe, transforming the latter into a Section One puppet.