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?

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.

Nikita is promoted to team leader early and is sent on a much more dangerous than expected mission with a disobedient operative.

Section believes that an imprisoned terrorist leader is ordering an attack through his lawyer. Nikita and Michael go undercover as a couple, and Nikita is supposed to be a psychic. The terrorist's lawyer asks Nikita to contact his dead son, but Nikita is shocked to discover something else.

A Section operative known as Terry fails a mission and admits to Nikita, the cause was her pregnancy. When she is teamed up with Nikita and Michael, she plans to escape from Section, and Nikita must choose a side.

Michael is captured and interrogated by terrorists, then loses his memory and does not know who he is.

Michael and Nikita are sent on a mission along with former hit man David Fanning, but during the mission he takes Nikita hostage and demands that Michael return his wife, or Nikita will be killed.

Section captures a mathematician in order to decode a code that is aiding terrorists in their attacks.

Section is trying to stop a terrorist group from engaging in suicide bombings, and Nikita is assigned to recieve information from an agent known as Formits, who, unbeknownest to Nikita, is in fact a serial killer.

Section falls into a trap when a mission to take out a Red Cell munitions base causes a virus to be spread throughout Section.

A new recruit named Andrea is romanced by Michael. When she learns that it was just a setup to gain allegiance to Section, she wants Nikita's help for revenge. Upon Nikita's refusal, Andrea proves dangerous to both Nikita and Michael when their mission ends up in a dangerous lab containing viruses.

Operations orders a raid to capture the leader of a terrorist group, which turns out to be a sentient computer.

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.

On an assignment to capture a Red Cell agent known as Jenna, with valuable information, Nikita is arrested and brought to jail in order to serve time, where Jenna is also serving time. But she is forced to betray the trust she has with Jenna when she must escape the jail along with her, only for Jenna to be captured and interrogated.

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.

During a mission, Michael is forced into a stage where he must cut communication with Section and complete the mission at any cost, but the target of Michael captures Madeline, and Operations is willing to kill Michael in order to protect her.