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.

Operations believes Nikita is a threat to Section, and wants to kill her during a mission. She survives his plot, and when she returns to Section, she looks into the disappearance of Michael, and finds what she didn't expect.

Nikita has a new mission, to get David Henderson Williams, Vacek's associate. She also learns more about Michael's history with Elena & Simone. Elena offers Nikita to stay with her & Michael. Nikita accepts, but she doesn't feel too cozy after her thoughts & memories get the best of her. More problems come about as Vacek misses a meeting.

To flush out Vacek, Operations and Madeline order Michael to poison Elena, but Michael can't bring himself to do it. So Section poisons Elena anyway, while Michael is out on a mission, and her survival will depend on whether Vacek has enough conscience to visit his daughter in her time of need. Meanwhile, Section moves sleazy informant Mick Shtoppel in as Nikita's neighbor.

After effectively losing his wife and son forever, Michael's performance begins to seriously suffer. So as Nikita seeks to restore Michael's will to live and to protect him from Section's latest enemy, Operations and Madeline bicker over what is the best strategy to handle fragile Michael. Meanwhile, Birkoff goes to Walter about a file Birkoff discovers, a file that contains incriminating evidence on Operations.

Section goes after Ivan Chernov, a terrorist who trains kidnapped children to do his dirty work. Michael sells Nikita to Chernov, who she discovers wants her for cloning experiments. Birkoff finds his life threatened by Felix, an abeyance operative who is extremely upset about being in abeyance. After returning to Section, a comment from Madeline makes Nikita think that Section might also be doing cloning. After some investigating, she discovers a room full of children, one of which looks identical to herself as a child. When she returns with Michael a while later, the room is mysteriously empty.

Section goes after Nikolai Markali, a politician whom Operations correctly believes is connected to the terrorist organization, Badenhein, although the suspicions at first appear to be unfounded. Other than these suspicions, he appears to be a man whose only crime appears to be being married to Operations' ""widow,"" Corinne - the woman Operations was married to when he ""died"" upon his recruitment into Section. Madeline, posing as a therapist taking over Corinne's case, and Michael, posing as a therapist slowly drive Corinne insane using a highly addictive ""medication"" which makes her extremely unstable and an altered videotape making it appear Nikolai was having an affair with Nikita. According to the mission profile, Corinne takes her husband's life.

Nikita is acting out of character. Michael observes she is pre-occupied, and when mission tapes of a disastrous mission show, the enemy was avoiding shooting her, he believes she is working for Red Cell.

A new operative with a photographic memory is brought in to ""remember"" the directory of a terrorist organization. When he is made a permanent recruit, Nikita looks into her own recruitment, wondering if it was planned or not.

Nikita, Walter, and Birkoff consider mutiny when Operations' orders become more and more illogical.

Brothers Karl and Simon Peruze are responsible for some of the most vicious attacks on civilians ever recorded. Eliminating both of them proves difficult, since neither brother would ever give up the other. Section One kidnaps Karl, wipes clean his short-term memory, and places Nikita with him when he comes to, so she can pose as his fiancee and lead Section to Simon. Strangely, the more Nikita learns about Karl's cruel history, the more she is drawn to him, falling in love with him. However, Nikita's slowly dawning realization that her mind is being controlled by Section threatens to unravel the entire mission.