Madeline has decided that Michael's romantic involvement with Nikita is affecting his performance, and so she sets about putting pressure on Michael to halt the relationship. Soon enough, Michael is no longer in charge of Tactical Oversight, so he loses his office, and is no longer running missions. He's replaced by Davenport, a decent guy who's now in charge of field operations. Can Michael give up all the power he's earned in Section One for Nikita? And will Nikita let him give it all up, even if he wants to? Meanwhile, a sultry operative by the name of Valerie is putting heavy moves on both Walter and Birkoff, which soon enough puts a strain on their friendship.

Literally playing with fire, Michael and Nikita are setting up clandestine rendezvous on Section missions as a way to get around Operations and Madeline's ban on their seeing each other (See Third Party Ripoff). Operations and Madeline still suspect Michael and Nikita of seeing each other on the side, so Madeline starts sending Davenport along on Michael's and Nikita's mission to spy on them. Meanwhile, Madeline orders Birkoff to sweep Michael's and Nikita's computer panels for secret communication, and when Birkoff does indeed discover communications between the two, it implicates Walter as their go-between. Will Birkoff turn in Walter? And, if so, what will happen to Michael, Nikita and Walter?

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.

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.

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.

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.

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?

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?

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?

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.

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.