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."

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 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 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.