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.

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.

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.

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.

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.

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.