Still reeling from the tragedies resulting from the disclosure of her role as a Section One internal investigator, Nikita is paired with a new partner by the head of Center and put back in the field, where she faces danger from all sides.
Quinn creates a holographic version of Madeline. Operation's obsession to work with Madeline again threatens to destroy Section One. Nikita discovers clues involving her original recruitment.
Although he no longer works for Section One, Michael remains Nikita's only hope for finding a cure to the deadly aftereffects from a mind-control process.
Mr. Jones must leave Center's protection to thwart the sale of deadly biological weapons. Nikita seizes the opportunity to force him to tell her the truth about her recruitment into Section One.
With the head of Section One, Nikita attempts to track down the mole who has been passing data to the Collective. She narrows the suspects down to two high-level colleagues, but one is killed whilst the other is in custody. In fact, the mole is far closer to home.
Nikita's relationship with Mr. Jones leads Operations to attempt to kill Nikita. Nikita threatens to report Operations' betrayal, but he has evidence that she helped Michael escape from Section One.
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.
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.
