After Substation three is destroyed by self-destruct, Section One investigates and finds a trace to Red Cell. What they also discover is that Red Cell has been taking similar blows. Operations decides to become allies and for each other to send top-notch agents. Operations sends Madeline, though Operations is willing to risk her.

While on her mission, Nikita gets shot. She was badly injured. Michael goes to the spot where she fell of the building's roof, but she isn't there. A man by the name of Henry takes out the bullet from her body, declaring he is a doctor. This guy won't let her go because he thinks she would want to stay after he helped her. She tries to break free, but she gets recaptured by him & his mother. Michael decides to go out to find Nikita. Henry wants to marry Nikita now, she wakes up in a wedding dress. He expects her to marry him after he rescued her from dying. Michael comes in time to help Nikita. He takes her with him to a serene campsite.

Nikita is injected with a psychotic drug. It causes her to think & see things that don't happen. For instance, when she was eating in a restaurant, she sees a guy coming with a knife towards the other man, but it never happens. She sees blood on her hands one minute, then the next, it is gone. She was given this drug to help her get into the institution, where Crystal French's son, David French, is at. Nikita still has the drug in her body, so Michael gets her out of mission before something bad happens. She receives electroshock therapy causing her to forget the mission. Nikita falls asleep, thinking she is still in the Institution, but she is safe in her apartment again.

When Nikita fails to assassinate Grenet, a Red Cell agent, and is unknowingly injured, Michael goes to her apartment to have dinner. It ends in disaster, when his water is poisoned and Nikita hands him over to Red Cell in exchange for his cornia files. She deletes herself from Section's databases and escapes to where they can't find her.

Michael and Nikita have been traveling from place to place, keeping one step ahead of Section One's attempts to find them. When George is eliminated from the picture after leaking intel to Red Cell in order to discredit Section One, the newly-empowered Operations and Madeline finally track down Michael and Nikita. They bring them back to Section. Just as Michael and Nikita are about to be cancelled, all of Section's systems suddenly stop. Mr. Jones, the mysterious head of Center, is on his way to Section One in order to conduct an evaluation, and has put Section in stasis. When Jones arrives, he is really Nick Shtoppel Nikita's neighbor and Section informant. He reveals that Nikita has been secretly working for Center for the last three years. Nikita assists Jones with his evaluation, and things change radically. Operations is forced to remain at Section One for the next seven years. Madeline takes her own life rather than be cancelled. Walter is transferred to the Farm, where he will

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 that besides the terrorists, she must deal with O'Brien & the hostility of much of Section personnel because of her role in Center's evaluation of Section.

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." Has Michael or Nikita's real father given her the information she needs to beat these after effects? Or is Nikita inevitably heading to the same place Adrian ended up, namely the grave? Meanwhile, O'Brien betrays Nikita, by revealing her deteriorating health to Operations, but unsure that O'Brien will be able to resist Nikita's "charms" any more than Michael did. Operations 'shadows' O'Brien with his very own 'pit bull' operative, Golliak. And Section One continues to try and crack "The Collective."

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. Was Operations telling the truth in "Deja Vu All Over Again" when he told Nikita that "Mr. Jones is not what he appears to be...?" Is Nikita making a big mistake in pushing the issue? Meanwhile, Quinn continues to put the "moves" on Operations, but what is she really up to?

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. Jones' two candidates: Operations or Marco O'Brien. Mr. Jones thinks it's the latter, but Nikita suspects the former. So Nikita sets out to find the "mole." Meanwhile, the two co-heads of The Collective, Graff and Haled clash over tactics, and whether to trust their "mole's" intel about Section One. Michael finally turns up, but not until the last scene!

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." While granting to Mr. Jones the theoretical possibility that Michael may be alive, Nikita denies that he would never be the "mole" for The Collective, Graff and Haled. Meanwhile, Operations sets out personally to see to it that an anti-Collective mission goes according to plan, but it's The Collective that is poised to blow Operations' plane out of the sky! Can and will Nikita save Operations' butt, one last time or should she even bother?

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. While new missions continue against The Collective with Michael's return, Nikita admits that she lied to him in "Four Light Years Further," and that she does indeed love him. Operations discovers that The Collective has infiltrated Section's mainframe to try to locate and kidnap Michael's son Adam, in attempt to re-assert control over him. Can Operations foil The Collective's plans?

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. Nikita & Michael do so, but this isn't good because Haled isn't alive anymore. This doesn't look too good for Michael. Two new candidates, Myra Mauk & Kelley are hoping for a spot at Section. Walter didn't have the best history with Myra, so he asks Jason Crawford to take her out of the running, he does so. More trades are offered later in the episode. Nikita is now running Section One, she lets Michael go to spend time with his son. Nikita says good-bye to Michael & continues are duties at Section One.