Mr. Jones agrees to surrender to The Collective in return for the release of Michael's son and Nikita's promise to take control of Section One. The Collective kills Jones and frees Adam. Nikita and Michael bid each other farewell . . . for now.
When Operations temporarily leaves Section One, Michael assumes full command. But will Michael's newfound power forever change Nikita's feelings towards him?
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.
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.
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.
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.
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.
Michael asks Nikita to bring him back into Section One, but Mr. Jones doubts Michael's motives. Michael's son, Adam, whom Operations has kept hidden from Michael, is kidnapped by The Collective, which ransoms the boy for Jones.
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.
Former neighbor Carla and her boyfriend Steven kidnap Nikita and take her to a cottage in the country owned by Adrian, the founder of Section One and the only person to successfully leave it.
