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.

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 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?

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.

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.

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.

When the founder of Section One comes back to destroy her own creation, Nikita must make a choice between the life of Michael or the existence of Section.

With Adrian's help, Nikita manages to breach the most sensitive area of Section and secure a file, code named Gemstone, which contains evidence which will bring down Operations and destroy Section One. Meanwhile, Operations forces Michael to identify the Section operative most likely to work with Adrian to undermine Section, Nikita. Michael confronts Nikita in order to try to find a way to protect her, but she denies any association with Adrian. Now Michael is forced to kidnap both Nikita and Adrian and bring them back to Section, knowing that Nikita and Adrian will be cancelled and that the incriminating Gemstone file will be permanently erased.