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.

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?

Glass Curtain is a high-tech terrorist organization that attracts new members via internet chat rooms. Posing as a new recruit, Nikita is taken to Glass Curtain headquarters, where she discovers that Michael's wife Simone is being held hostage. A former Section One operative, Simone was believed killed years before. Now, Michael's continued love for Simone may threaten the success of Section One's attempted infiltration of Glass Curtain.

A nuclear trigger is stolen by a cold-blooded terrorist couple responsible for killing an entire team of Section One operatives. In an attempt to retrieve the trigger, Nikita poses as the wife, Helen's long-lost daughter, who was put up for adoption because Helen was in prison at the time of her birth. However, this leads to unexpected consequences for both "mother" and "daughter."

While working undercover near a Central European Consulate, Nikita is confronted by a known serial rapist. Nikita easily subdues the man, leaving him battered and bruised. O'Brien, the police detective on the case, has been pursuing the man for years, and realizes that the rapist's victim was no ordinary woman. With the help of a witness he manages to break through Nikita's cover story and track her down. O'Brien now knows the truth about Nikita, he will have to be cancelled, unless Nikita can turn the situation around to her advantage.

Section One is assigned to protect Jovan Mijovich, a politician attempting to negotiate peace among opposing forces in his section of the world. When Nikita meets with a contact to find out who has attempted to assassinate Mijovich, Nikita is recognized by Julie, a childhood friend. Nikita attempts to protect Julie's life by creating a new identity for her, but Julie is actually an operative for the organization attempting to assassinate Mijovich.

Nikita is assigned to get close to a money launderer in order to steal his data files. When she learns about his successful charity for troubled youth, she starts falling in love with him. However, when Section One admits to Nikita that the shelters are a front for a thriving child slave trade, Nikita's loyalties become divided.

The CIA believes that a rogue element of their agency is responsible for a recent massacre of heroin dealers, performed in order to steal money and drugs as part of an embezzlement scheme. Section One is brought in to clean the house quietly, but Nikita's continued involvement with architect Gray Wellman is tampering her ability to be a reliable operative. As Section One's operation reaches a fever pitch, Nikita is unable to balance both sides of her life, and is forced to make a choice between the organization that controls her life and the one man that she's ever loved.

A live nuclear warhead is smuggled into the states and the only witness to the act is a mentally challenged pizza driver named Rudy who witnessed the transfer. A transmission claiming that the warhead is armed in a random city and will detonate in 24 hours is intercepted and Section uses Rudy to determine who the man is that brought the warhead into the country - a traitor in the Agency. The location is discovered and with Rudy's help, Birkoff is able to determine the code that will disarm the bomb in time. Rudy is allowed to live due to his help and is allowed to leave Section with Nikita's assurances that he will never tell anyone of Section or it's whereabouts.

When Nikita is sent to investigate a bartender at a posh club who may be a terrorist contact, he responds to her questioning by leaping from the 65th floor window to his death. A search of his apartment turns up a strange helmet-like device, which Section later discovers is used for brainwashing. Unfortunately, Nikita has used the device several times in an effort to discover what it is, and now it is in control of her mind. When Nikita and other operatives are assigned to protect the Premier of China from other similarly brainwashed individuals, Section has no idea that the greatest threat to the Premier is Nikita herself.

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.

Jovan Mijovich has been elected as premier of his new nation, but there is a hit man out to assassinate him. Nikita and Michael, along with other Section One operatives, are dispatched to provide security. During the inaugural celebration, the hit man is taken out, but a hostage situation develops that no one expected. A man, Bruner, claims Mijovich raped and blinded his daughter during the nation's civil war, and threatens to kill him. Nikita tries to defuse the situation, and manages to keep Mijovich alive for the time being, but when Bruner's daughter appears to give her side of the story, the accuracy of her testimony will mean the difference between peace and war for her people.

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, a girl living on the streets, is wrongly accused of a murder she did not commit and sentenced to life in prison. After the government arranges to fake her suicide, Nikita wakes up at Section One, a top-secret agency that aims to train her to become an anti-terrorist operative. Nikita wants to resist, but in order to stay alive, she has no choice, but to comply with their plans.

Section One is assigned by the CIA to ""quietly"" deport Suba, a foreign anti-terrorist contact who is smuggling waste uranium out of the country for his own profit. The first attempt to capture him goes terribly awry, and Nikita is held responsible. Upon further investigation, Nikita discovers a traitor in the Section, but one who is being manipulated by Suba is holding his son hostage. Nikita must now decide whether to risk the wrath of Section One by rescuing the ""traitor's"" son.

A mysterious Section One operative offers Nikita a seemingly ironclad opportunity to escape from Section One for good. All the information he gives her checks out, and Nikita seriously weighs his offer. However, Michael states making romantic overtures toward Nikita, and her emotions are divided. Is the Section just toying with her to test her loyalty, or is it the opportunity to escape a real one?

Section One's computer security is breached and the directory of all their agents is stolen. Michael goes to Prague to reclaim the directory, but the man who stole it is killed by another terrorist seeking the directory for himself. Nikita discovers that it was randomly left with a civilian passenger on a Prague city bus, architect Gray Wellman. Nikita is assigned to Gray in order to get close to him and retrieve the directory, but when she starts falling for him, her actions not only threaten the mission, but Section One's very existence.

Section captures a mathematician in order to decode a code that is aiding terrorists in their attacks.

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.

When an international arms smuggler steals a canister of deadly nerve gas, Nikita and Michael pose as a married mercenary couple in order to infiltrate his compound. However, when the gas is discovered wired to a bomb in a crowded train station, Nikita must put her life on the line to defuse it.

One of the members of a criminal organization that steals classified information to sell to the highest bidder is Operations' long-lost son, Steven. Section One's mission is to eradicate this group along with a dangerous terrorist that plans to buy a smart missile chip from them, but Operations asks Nikita to keep Steven alive at all costs. Nikita agrees, only if Operations will let her finally leave the Section for good. He agrees, but Nikita threatens to kill Steven if Operations doesn't keep his word. Unfortunately for Nikita, she is unaware of Michael's true role in the mission.

Nikita and Michael are sent on a mission to take out someone in a Balkan nation, but Nikita must force Michael into protecting two displaced children, however that protection prevents Nikita from hitting their target, and they must risk their lives in order to get him down.

Operations orders a raid to capture the leader of a terrorist group, which turns out to be a sentient computer.

Nikita is assigned to evaluate Karyn, a recruit who is nearing the end of her two year training period. During her first live mission, Karyn kills her mentor, Brian, in cold-blood. When Nikita confronts her, Karyn confides that Brian had repeatedly raped her during her training. This reason, coupled with the fact that everyone in Section One seems to like Karyn, makes Nikita more insecure about her decision whether Karyn should have full status or be cancelled. Nikita realizes that Karyn is definitely not Section material when Karyn exhibits psychotic behaviors during a mission and decides that Karyn should be cancelled. Operations and Madeline inform her that Karyn was already set for cancellation, they were just testing Nikita and if she had made the wrong decision, she too would have probably been cancelled.