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.

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

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?

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.

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?

The unbelievable happens! Nikita is called before Operations and Madeline and is given fantastic news, she's free! As part of a ""pilot program,"" Nikita is granted her freedom and a normal life, as long as she never contacts anyone from Section again, and as long as she agrees to be regularly evaluated. Nikita is skeptical at first, but after 6 weeks on ""the outside,"" she starts to believe that maybe this is for-real. Sure enough, George from Oversight shows up with the strings, in exchange for her freedom, Nikita must do one thing, return to Section One to kill Operations! The man whom George claims killed Nikita's real father. Will Nikita do it?

Operations gives Michael and Nikita an almost impossible task; they must get five absolutely, brand spankin' new recruits (Aaron Ashmore, Clé Bennett, Kira Clavell, Megan Fahlenbock, Brian Poth) up to full, field-level operatives, in a very short amount of time! They must go up against new terrorist group, Crystal Sky (who recently did a number on Section Eight). Nikita doesn't think it can be done. Is this another of Operation's gambits, in which the five new recruits are cannon fodder for some mission? If so, can Michael and Nikita save them from this fate? And, if these recruits aren't ready by the time of the mission, could their inexperience also put Michael and Nikita themselves in peril?

Birkoff creates an Artificial Intelligence (A.I.) program to serve as his replacement, when he's away. In fact, Birkoff is up for a large batch of downtime, when a critical situation arises and Operations cancels Birkoff's downtime. Birkoff's A.I. program, which is just a little too attached to old Seymour, doesn't take this news well, and proceeds to take matters into its own hands. The A.I.'s solution to Birkoff's predicament is to kill everyone in Section One, except Nikita, so Birkoff can escape with Nikita as his companion. Can Birkoff save Section One before his A.I. program carries out it's insane plan?

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.

Seeking a lost command clone (a computer-like device that apparently allows the user to command a Section without outside aide) that was apparently captured by Red Cell and then stolen by another terrorist group, George and Oversight orders Section one to work together with an agent from Section Four to search for the missing ""command clone."" What is Section Four? Apparently, it's the Section where people/agents with extrasensory abilities are developed. So, who is the agent from Section Four? None other than a 12-year old boy by the name of Gerome. Of course, with his extrasensory abilities, Gerome soon overwhelms the ability of Madeline and Operations to control him. Can Nikita bring Gerome under control before he destroys Section One?

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.

Another incursion takes place in Section One, this time in the form of a virus that is making Section One's members sick, one by one. Taking matters into his own hands, George orders in his own Bio Team to treat Section's members. Operations suspects George has an ulterior motive. Sure enough, when Section's people, starting with Walter, followed by Nikita, go in for their ""examination"" with George's Bio Team, they come out vegetables. It seems George's team is mind wiping (downloading the contents of the brains) the Section's members. This process causes them to relive their lives, before leaving them vegetables. Can Michael and Birkoff stop George's team before everyone in Section One gets their brain sucked?