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.
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.
When Operations temporarily leaves Section One, Michael assumes full command. But will Michael's newfound power forever change Nikita's feelings towards him?
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.
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.
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.
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.
