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.

With Michael's help, Nikita survived the destruction of a Freedom League hideout in the first season's final episode. Since then, she has been on the run from Section One. While working as a waitress, Nikita is captured by the Freedom League and used as bait to lure Section One into a trap. During a raid by a Section team led by Michael, Nikita saves Michael's life and they manage to escape together. Later, on an abandoned ship, Nikita and Michael share a night of passion. However, Michael's lies about Nikita's whereabouts are in danger of being exposed.

Birkoff may have stumbled on Section One's biggest coups yet, a chance to nab a top Red Cell operative by the name of "The Cardinal", who has eluded Section One for more than 15 years. Unfortunately, Birkoff's arch-nemesis Greg Hillinger is convinced that Birkoff is wrong, and Hillinger convinces George that Operations and Section One are walking into a trap. Based on Hillinger's intellect, George moves against Operations on the assumption that the operation against The Cardinal is bogus. Is Birkoff right after all? And if Birkoff is wrong, is this the end of Operations, and Birkoff too?

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.

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?

Nikita continues to show evidence of the "reprogramming," including ordering the elimination of a captured Section operative and endangering the lives of children during a mission, and taking part in the beatings of a captive. Michael is determined to reverse Nikita's reprogramming, and he soon determines that the former Section operative who came up with the "reprogramming" process, Ross Gelman, may be the key. Meanwhile, Operations couldn't be more proud of the "new" Nikita, but Madeline is still worried. Eventually, Operations concludes that Michael's attempts at restoring Nikita have gone too far, and takes extreme measures.

Michael kidnaps Nikita with Walter and Birkoff's help, and manages to reverse Gelman's process. Together, they outsmart Madeline and Operations leading them to return to Section.

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.

Michael escapes Red Cell and is assigned to meet Nikita and kill her, however she doesn't show up and an Alpha Team is assigned to track her down. Michael leads the team with Kate Quinn. Before the mission, Michael discovers Quinn is Nikita and that he could leave Section. The Alpha Team is wiped out and Michael escapes with Nikita.

After Michael eludes Operations' first cancellation attempt, Operations puts all missions on hold and sends out a team to kill him. Michael again manages to escape certain death, but this time he returns to infiltrate Section. Determined to find the files that possess the formula for deprogramming Nikita, Michael is stunned to discover who Section's first test subject was; Adrian, Section One's founder, whose effort to topple Operations failed two years earlier. To gain leverage against Operations, Michael kidnaps Adrian, but her help proves limited when Michael discovers her mind is gone.

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

Section One is hot on the trail of Tyler, one of the world's most dangerous terrorists. After Tyler kidnaps a young inventor who has created a new, completely un-detectable plastic explosive, Nikita is sent to try and rescue the inventor and keep his knowledge out of Tyler's hands. When the mission is unsuccessful, Nikita is given orders to cancel the inventor, but she refuses. Operations decides that Nikita has crossed the line, and he purposely sends her on a suicide mission to destroy a terrorist hideout. Michael intervenes and gives Nikita the means to escape, but her freedom will change both of their lives forever.

Michael discovers that Adrian's mind is not blank as he thought it is. Together they try to save George from Operations and Madeline's attempt to assassinate him. Meanwhile, Michael kidnaps Nikita in a futile effort to reason with her.

Section One is finally moving hard against Red Cell. Their objective is to capture Chief Strategist (Madeline's opposite) in Red Cell, a man code-named Leon. Once captured, Leon and Madeline begin a dangerous game of mental and emotional cat and mouse. Is Madeline actually developing an emotional attachment to Leon that is interfering with her objective? And what is with the incision that Birkoff discovers behind Madeline's ear? Meanwhile, Birkoff is giving Walter the cold shoulder, and continues to investigate the whereabouts of his twin brother, Jason Crawford.

Michael is keeping track of Elena and Adam, and he becomes concerned when a new man enters their life. Sure enough, the man turns out to be a Secion One "Valentine Operative" by the name of Robert Corliss whom Operations has sent into to get Elena's Uncle, Stefan Vacek. It seems Uncle Stefan is taking over Elena's father's old terrorist business. Can Michael protect Elena and Adam once again without being exposed as still being alive? And can Corliss be trusted with Elena and Adam?

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 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 stolen Directory has ended up in the hands of Red Cell, and operatives are being hit around the world. Section is being forced to evacuate. In order to learn Red Cell's next move, Nikita and Michael attempt to capture Red Cell's next move, Nikita and Michael attempt to capture Red Cell's counterpart to Birkoff, but instead, they themselves are captured and tortured. Neither of them are willing to divulge Section's current location, but when Michael admits his love for Nikita, she breaks, because she can not stand to see Michael tortured any further. Far from destroying Section One, Nikita quickly discovers that this was the intended plan all along, and Section has a big surprise for Red Cell.

Nikita continues on the mission she was sent on in, "Man in the Middle," which is to marry Helmut Volker, a man with several ties to Red Cell, but she finds out that she is not the only one with secrets, her new husband has a big secret of his own.

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!

During a mission to destroy a Russian chemical plant, Michael is injured and is left behind. Section determines that it is too risky to save Michael, but eventually does go to find him by sending Nikita and Madeline in as travelling cosmetic saleswomen. Meanwhile, Michael kidnaps a nurse, Angie Georgiev and convinces her to help him before the head of the secret police, Egran Petrosian, is able to find him. Madeline and Nikita are able to determine where Michael could possibly be and arrive at Angie's apartment shortly after Petrosian does and extract Michael and Angie with Petrosian in pursuit. The four arrive at an abandoned airstrip to await air transport from Section when Petrosian's forces arrive, killing Angie in the fighting that ensued. It is later revealed that Petrosian is really a Section operative that has been in deep cover for the past 17 years. The ""rescue mission"" was really means to extract Petrosian from deep cover and bring him back into Section's fold.

David Fanning is one of the world's most dangerous hit men, but Section One is powerless to stop him. Fanning possesses ""The Book,"" a collection of top-secret information damaging to Western governments, and if the Section makes any attempt on Fanning's life, the Book will be released automatically. When the Section's only way in is through Fanning's abused girlfriend, Nikita and Michael are forced to use any means possible to secure her loyalties, but her emotional instability could prove fatal to both of them.

Section's newest target is the son of a wealthy industrialist, by the name of Helmut Volker, who is supplying drugs at his parties when not funneling arms to Red Cell. The twist is Operations and Madeline have figured out that Michael has "restored" Nikita, so Operations uses this operation to once again drive a wedge between Michael and Nikita. Helmut Volker must marry if he is ever to inherit hit father's business, so Operations orders Nikita to marry Helmut when he proposes! Meanwhile, Michael does everything he can to prevent that from happening.

Operation calls Michael and Nikita out on a favor, he orders them to protect a Vietnam vet by the name of Willie Cain, a man who is now little more than a drifter and a bum, from the thugs who are out to get him in a deal gone bad. Operations believes that he would not have survived capture and torture in Vietnam without Willie's help. What Nikita and Michael don't know is that they are embarking on a mission that will mix them up with Operations' Vietnamese torturer, Fan Van Lin, Carlo Bonaventure the head of a Mafia Crime Family. Meanwhile, Birkoff develops a sudden interest in how he became part of Section, the place he has been in all his life. An interest leads him to the discovery of an unknown twin brother, and a duplicitous history involving Walter.

An important Center satellite named Comstat Alpha crashes near a small town in Kentucky by the name of Dingman's Hollow. Michael and Nikita are then sent on a mission to retrieve it; the first mission with Birkoff's replacement, Corman. The data it carries, before it falls into the wrong hands. When Michael and Nikita get to Dingman's Hollow, they discover that the satellite is missing from its crash location. Soon enough, Nikita discovers that strange things are afoot in the town of Dingman's Hollow. It turns out that the entire town is a ""Sleeper Base"" for the Black Storm terrorist group, making Michael and Nikita's mission that much more difficult. Meanwhile, Naomi, the girlfriend of Birkoff's brother, Jason Crawford, is taking him to Aruba. Can Section One be far behind?