Nikita is sent back to Section One to destroy a new terrorist threat that only she can deal with which is a summit meeting of representatives from several terrorist groups. She is teamed up with a new level 5 operative, Marco O'Brien. O'Brien was the police officer recruited four years earlier because of a mistake Nikita made, a fact that O'Brien has not forgotten

Nikita finds clues about why she was recruited into Section. Is it possible her father was an operative, codenamed Flavius, and that she has a sibling with the initial "M" who is somewhere in the covert world she lives in? Quinn redesigns Birkoff's Artificial Intelligence program to build a holographic replica of Madeline, complete with Madeline's memories and psychological profile. Although Operations is greatly pleased to have Madeline at his side once more, it soon becomes clear that despite it's complex programming, it is just not capable of being Madeline because it doesn't have her instincts

After the explosion at the house of Nikita's father, Nikita enlists Walter, and then Jason Crawford, to decript its contents. The result; the location of the convelecence home where Michael took Adrian after the "Gelman Process" mess. And this just happens to coincide with Nikita's physical deterioration because of her experience with the "Gelman Process

After someone breaches Section and breaks into her room, Nikita is more determined than ever to find out the truth about why she was brought into Section. She arranges to get at Mr. Jones personally by having him go out as "Mick Schtoppel" on a mission against an arms dealer with ties to The Collective, by the name of Massima Valenti

Nikita finally comes face to face with her father, the real Mr. Jones, but rather than being an "emotional" reunion, Mr. Jones is all business, and immediately sets Nikita out on a new mission; finding The Collective's "mole" in Section One! Mr

Nikita and Mr. Jones have The Collective's "mole" narrowed down to four suspects: Operations, Quinn, Walter and the late Marco O'Brien, but Mr. Jones has a fifth possibility that Michael Samuelle is still alive, and that he is the "mole

The situation is dire as The Collective, still led by Graff and Haled, is cleaning Section's clock. But, just in time, Michael asks Nikita to help him return to Section, where his re-emergence is viewed with suspicion by both Mr. Jones and Operations

Michael's son, Adam is a hostage of The Collective. Michael must save his son in a trade proposed by The Collective. Meanwhile, Haled is confronted by Michael on an offer to get rid of Graff, then leading Haled to become the head employee