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.

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.

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.

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."

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.

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.

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.

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.

Section was informed that the water of the city would be polluted if the United Coalitions needs weren't met. Gregor Kessler, the one with many aliases and disguises, steals the Cobalt 60. Kessler was offered money to get the Cobalt 60, reported by a spy of Section. Gregor dresses up as an aged lady to get through South American Customs. Kessler manages to capture the Cobalt 60, but Madeline confronts him. Some how, he knows about her past and starts intimidating her. Section takes Kessler's daughter in hope to retreive the Cobalt 60. This doesn't work for him because he kills her, so Section can't hurt her. Meanwhile, Nikita finds out more about Madeline's past & what she did to her sister. Madeline never wanted anyone to know about it. Kessler now wants Madeline, Section doesn't want her to go by herself, so they stand by in a nearby distance. Madeline falls into a hole where Gregor is. He grips her up by the neck, but she breaks free. It wasn't really her, it was Michael dressed up

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.

While on a mission to tag a stockpile of Stinger missiles, the Section van is breached, and Birkoff is forced to defend himself for the very first time. Now, his fear of being killed on future missions is interfering with his ability to protect Section operatives, unless Nikita can help him overcome this fear, Birkoff is in danger of being cancelled.

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 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.

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.

While Nikita is reassigned to Special Operative Jurgen, Section is contacted by one of Freedom League's operatives in order to verify Nikita's story about her capture.

Section believes that terrorists are after the nuclear power source of a downed satellite. They later discover the terrorists are actually after it because it is a military satellite and it will give them access to the Pentagon if they are able to salvage it and crack the codes. Nikita grows closer to Jurgen and Section uses it to their advantage.

Egram Petrosian, the former Section deep cover agent rescued by Section One, takes over and promotes Nikita to second in command when Operations is seriously wounded by an insane operative.

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.

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.

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.

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.

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.

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.

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.

Nikita is brought back to full operative status when Birkoff discovers a six-man terrorist team are making several random attacks.