Nikita, a girl living on the streets, is sentenced to life in prison for a murder she did not commit. When the government fakes her suicide, Nikita wakes up in Section One, a top-secret agency that plans to train her as an anti-terrorist operative -- and she must comply in order to stay alive.
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 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 a final attempt to retrieve the trigger, Nikita poses as the couple's long-lost daughter, who was given in adoption years ago. However, this leads to unexpected consequences for both "mother" and "daughter".
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 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, who 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.
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 hampering 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.
Section One has successfully destroyed a chemical weapons plant in a former Soviet Block country, but in the process, Michael is wounded and left behind. On the run, he hides in the house of nurse Angie Georgiev. To rescue Michael, Nikita and Madeline pose as cosmetics saleswomen in order to enter the country. Once there, Madeline induces a heart attack in order to be admitted to the hospital where they think Michael is. But when Madeline's cover is blown by a high-ranking military official, Michael must convince Angie to risk everything to help them escape.
A terrorist group smuggles a live nuclear device onto North American soil and threatens to detonate it in a major city. However, the bomb transfer was accidentally witnessed by Rudy, a simple pizza delivery man. Section One interrogates him, thinking he was involved, but Nikita believes Rudy's story--that he was in the wrong place at the wrong time. Nevertheless, he will be cancelled--unless Nikita can demonstrate that without Rudy's help, the bomb will not be deactivated.
When Section One attempts to thwart the thief of a canister of Cobalt 60, they lose the Cobalt, but capture one of the world's most fearsome terrorists, George Kessler. To find the Cobalt 60, Madeline must interrogate Kessler, who successfully uses his knowledge of Madeline against her. She manages to gainthe upper hand by confronting Kessler with the daughter he never met, but whenhe kills her in cold blood and escapes, Madeline must put her life on the line and confront him alone.
Nikita is assigned to evaluate Karyn, who is coming to the end of her two-year training period. On a mission to capture a terrorist gone awry, Karyn kills her trainer in cold blood, then lies about it. When Nikita confronts her, Karyn confides that her trainer had repeatedly raped her. This, coupled with the fact that everyone in Section One seems to like Karyn, makes Nikita's decision all the more difficult. But Nikita's feelings aren't good, and she tries to discover the real story about Karyn.
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.
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 Michaels' true role in the mission.
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. Because O'Brien now knows the truth about Nikita, he will have to be cancelled, unless Nikita can turn the situation around to her advantage.
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 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.
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.
When Nikita is sent to investigate a bartender a 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.
While tracking down Tyler, a fearsome terrorist, Section discovers that the employee of one of tyler's contacts has invented a plastic explosive that is completely undetectable. When Tyler kidnaps the young man, Nikita and team are sent in to capture the inventor. The rescue goes awry, and Nikita is given orders to cancel him. She refuses. Operations decides that Nikita has finally crossed the line, and he sends her on a suicide mission with other operatives set to be canceled. Without Operations' knowledge, Michael 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 avenge Section One. During Section's raid, Nikita manages to escape and save Michael's life, and later on an abandoned ship, she and Michael share a night of passion. However, Michael and Nikita's lie about her true whereabouts is in danger of being exposed.
Nikita is reassigned to Special Operative Jurgen to retrain her after her capture by the Freedom League. When Section is contacted by Kudrin, a Freedom Leaguer who could verify Nikita's story, Section seeks to capture him for questioning. To keep Kudrin from revealing the truth, Michael deliberately attempts to kill him during the mission, but Kudrin survives, and Madelina as well as Jurgen start unraveling Michael and Nikita's lie.
Birkoff discovers that a seemingly random series of terrorist activities are being perpetrated by a six man mercenary army Section One dubs "Helix." Jurgen helps Nikita back to full operative status in preparation for Section's attack against Helix, but Michael is concerned about Nikita and Jurgen's growing relationship. Convinced Jurgen is manipulating Nikita in order to expose her, Michael and Jurgen come to blows.
Jurgen's freedom within Section One fascinates Nikita, and she continues to spend more time with him, despite Michael's disapproval. Michael warns Nikita that Jurgen is not who he claims to be, but Nikita ignores Michael's advice, and she and Jurgen grow ever closer. unfortunately, Nikita has become an unwitting pawn in a power struggle between Jurgen and the Section, which could mean deadly consequences for Jurgen... and Nikita.
A Section operative goes crazy and shoots Operations during a briefing. While Operations is on the verge of death in intensive care, Egran Petrosian -the deep cover agent rescued last season- takes over Section and promotes Nikita to second-in-command. Despite warnings from Madeline, Nikita believes that Petrosian is the better man to run Section One because of his straightforwardness. But when Petrosian asks Nikita to murder Operations, the future of Section hangs in the balance.
When Michael is sent to assassinate an arms supplier, the operation is breached, and Michael enters "mandatory refusal" - a situation where he must break off communication with Section and complete the mission at all costs. Unfortunately, the arms dealer kidnaps Madeline, and Operations believes the only way to protect her is to kill Michael if necessary. however, Nikita has other plans.
Section One attempts to stop a bombing at a schoolyard, and Nikita observes that Michael knows more about the nature of the bomb than he should. When Nikita questions Michael about this, he brushes her off, but Nikita knows he is hiding something. The next day, she follows Michael, and discovers that he is meeting the bomber. Michael and the bomber, Rene, were student protesters involved in terrorist activities in the 1980's, and their paths have crossed once again. But when Operations asks Michael to betray his friend, Michael's loyalties are divided.
Nikita and Michael are sent to a Balkan nation to assassinate Radovan Luka, an arms buyer for rebels who are waging a campaign of ethnic cleansing. When Nikita and Michael arrive in the country, they discover two displaced children, and Nikita forces Michael into protecting them. However, the children's safety distracts Nikita from her opportunity to shoot Luka, and now, Nikita and Michael must risk all their lives by infiltrating a Balkan death camp to kill him.
Red Cell has created a human time bomb. In order to discover the identity of the human bomb and its eventual target, Nikita must capture one of Red Cell's operatives, who is serving time in a foreign prison on drug charges. Nikita is sent to that country to get arrested and taken to the same prison. However, not only does Nikita have to secure the trust of Jenna, the Red Cell operative, but Nikita is forced to betray that trust by escaping the prison with Jenna through a series of underground tunnels, only for Section to abduct and interrogate her.
Because of a shortage of operatives, Nikita is promoted to team leader three years ahead of schedule. She is now responsible for all aspects of a Section mission: operative selection, planning, and successful execution. Her assignment is to capture a dealer in spent nuclear fuel rods, but intel is sketchy, and the mission is more dangerous than usual. To make matters worse, one of Nikita?s team, Vizcano, is unruly and disobedient. Nikita must find a way to control her, or run the risk of failing the mission.
Section believes that the imprisoned leader of a terrorist group is funneling orders for an upcoming attack through his lawyer, Armel. Nikita and Michael pose as an average suburban married couple in order to trick Armel into believing Nikita is a "retired" psychic. Convinced, Armel kidnaps Nikita and forces her to psychically "contact" his son, who died in a traffic accident. However, Nikita discovers that Armel’s son is very much alive, and being held by Section.
Nikita befriends a long time Section operative, Terry, who fails her assignment during a recent mission, and confides to Nikita that the reason was due to her pregnancy. But when Terry, Michael and Nikita are assigned to capture a rogue NSA agent, Terry betrays the mission in order to escape Section and have her baby on the outside. Now, Nikita must choose between the Section or protecting Terry and her baby.
Birkoff discovers that a terrorist group is using a code to tunnel into a Defense Department satellite and use it for seemingly unrelated terrorist attacks. The code must be broken in order to stop further attacks, but the NSA and even Birkoff are unable to decode it. Section kidnaps a brilliant but cocky young mathematician to solve the problem, but his uncontrollable nature poses a threat to the mission, Section, and ultimately, his own life.
Section must stop a terrorist group from the Mideast, Bright Star, from performing any more suicide bombings. Because these bombs are created from land mines, Bright Star's whereabouts are difficult to trace. Nikita is assigned to secure information from Formitz, who is responsible for creating all of Bright Star's false documents. However, when Nikita learns that Formitz is a serial killer, specializing in the brutal murder of prostitutes, her desire for retribution may threaten the lives of many.
A killer virus is accidentally unleashed inside Section One. Section sends a team to neutralize a possible Red Cell munitions outpost in Scotland, but when they arrive, they find the place abandoned. Michael and Nikita continue surveillance while Mowen, a Section op, takes samples and heads back to Section. Shortly afterward, Mowen falls deathly ill with a mysterious ailment. Operations realizes that the mission was a trap, designed to release a contagious deadly virus, which is quickly spreading through Section. Now, Michael and Nikita must choose between finding the antibiotic and saving Section, or the possibility of their own freedom.
After being captured and interrogated by terrorists, Michael's loss of memory puts him at risk of being cancelled. After an assault on a club, Michael is captured and interrogated by Red Cell tactitian Orlando Perez. On a second mission to secure Perez, Nikita frees Michael, but he cannot remember who he is or why he is in Section. Nikita covers for Michael, knowing that he would be cancelled if Operations found out. However, Nikita's job is made more difficult by the fact that Michael, not acting himself, is being emotionally honest with her.
Michael and Nikita are forced to go on a mission with a former terrorist hit man who, to their dismay, is now working for Section. Last season, Michael and Nikita brought down terrorist hit man David Fanning with the unwitting help of his abused wife, Lisa. Now, Section is using Fanning to eliminate an even more powerful terrorist, and Michael and Nikita are forced to go on the mission with him. However, the mission goes sour when Fanning takes Nikita hostage, demanding Michael return Lisa to him. Now, Michael must find a woman he used and betrayed for Section within 48 hours, or Nikita will be killed.
When Michael romances Section's new profiler, it causes tension between Michael and Nikita, threatening the outcome of an dangerous mission. Andrea, a young, arrogant mission profiler, is brought into Section, and Michael makes a successful attempt to romance her. This causes Nikita to lose focus, which almost botches a mission to secure the owner of a lab that creates lethal designer viruses. However, when Andrea learns that Michael's seduction was a setup to gauge her loyalty to Section, she vows revenge. Nikita's refusal to help her now puts both Nikita and Michael's lives in danger on the next mission-to the deadly lab itself.
Section captures the leader of a powerful terrorist organization - a sophisticated computer capable of independent thought. Whenever Section downgrades security in different areas of the world, a terrorist organization makes a successful strike in that area within hours. Concerned that the strikes may be the work of an insider, Operations orders a successful raid to secure the leader, only to find out that "he" is nothing more than a computer. Able to converse, the computer is interrogated by Madeline, who believes it is only capable of pure logic, not intuitive thought. However, when Madeline and Operations leave Section together, the computer has other plans, and Michael is forced to lead Section in their absence.
A terrorist's confidante turns out to be a Section operative thought dead. When Section discovers a wealthy terrorist plans to fund upcoming civilian attacks, Michael and Nikita pose as money launderers in order to stop him. However, his assistant, Giraldi, claims to be a Section operative who has been in the field for nine years and wants to be brought back in. When Nikita informs Operations, he tells her to ignore his request, but when Madeline finds out, she insists Nikita bring him in. Now, Nikita is caught between Madeline and Operations, and a man’s life hangs in the balance.
The founder of Section One kidnaps Nikita, and recruits her for the ultimate mission - to destroy Section, once and for all.
