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.
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.
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.