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.
Nikita finds a colleague in the new recruits, someone named Jamey. Jamey tells Nikita that if she helps him stay in Section, he'll lead Nikita to her mother, who has been looking for Nikita ever since she supposedly committed suicide in jail.
Nikita, along with two other operatives Mark and Angela, are kidnapped by a two-person sibling terrorist team. Both Mark and Angela are tortured, but Mark breaks during the torture and tells the terrorist duo the location of a Section sub-station. After being rescued, Nikita plans with Mark to lie to Section and try to defeat the brother/sister team on their own. But when her plan fails, Mark blames Nikita for revealing the information, and she is put under trial.
Operations passes over Michael for Chief Strategist in favor of a smarmy Section operative by the name of Zalman, and Michael is so furious that he plots with Nikita to escape from Section One. Indeed, after stealing a Section One "Field Router" Michael and Nikita successfully disrupt a mission against new Red Cell leader Vincent Tomas, and make their escape. Zalman is going to take the fall for Michael's and Nikita's escape, and he will stop at nothing to find them.
On an operation to get industrialist and terrorist financier Charles Meyer, Nikita is sent to a "modeling agency" run by Amalin Anagar, which is in reality, not just a brothel, but also an arena where beautiful girls are forced to fight each other to the death in a place called "The Pit" While undercover at Anagar's, Nikita tries to protect a naive young girl named Sondra from fighting in ""The Pit,"" while also trying to figure out a way to save all the girls at Anagar's (an objective which is not in the mission profile). Meanwhile, Madeline appears to be jealous of Renee from Oversight who is visiting Section One. She may have reason to be, as Renee immediately puts moves on the very willing Operations.
This time, Section is out to get an outfit by the name of The Alliance, and Section's way in is a psychotic courier by the name of Jan Bailin. Bailin has other plans and she kills herself before the Section can use her. So, as a backup, Section employs a meek, terminally ill lookalike for Bailin by the name of Sarah Gerrard. As she trains her, Nikita starts to get suspicious, did Section purposely make Sarah ill to make it easier for Section to convince Sarah to work for them? And if so, will Section even let Sarah live if she completes the mission?
After an operation against a terrorist group, Michael brings one of the terrorists back to the Section for questioning. The "capture" is a plant, and he knocks Madeline out during interrogation and runs amuck in Section One's HQ. Before Michael finds and eliminates the man, he successfully uploads many of Section One's crucial files, including the Registry (which is at least encrypted, and will take the terrorists several days to decipher) and the exact location (un-encrypted) of Section's HQ (located in Paris). Operations orders the evacuation and destruction of Section One's HQ. With Section in temporary quarters, Operations takes over the counter-operation personally, and goes out on a mission with a less than thrilled Nikita. Will Operations be able to find the terrorist base before the terrorists decode The Registry?
With the "situation in the Balkans" again reaching critical, Operations is called off on a consulting job in the field by "The Center," and he turns over temporary full control of Section One to Michael. Operations leaves Michael with one warning, George from Oversight wants a full-scale campaign waged against terrorist financier Luigi Bergomi, but Michael must resist this as Bergomi is too strong and would overwhelm Section forces. After meeting with George, Michael has a change of heart, and decides to launch an operation against Bergomi, despite Madeline's and later Nikita's strong objections. Has the absolute power of running Section One gone to Michael's head? Meanwhile, now that they are "officially" lovers, Michael promotes Nikita as his lieutenant over another agent named Wallace, and when Wallace turns up dead after an operation against Bergomi, Nikita wonders if Michael is playing favorites, and trying to protect her.
Madeline has decided that Michael's romantic involvement with Nikita is affecting his performance, and so she sets about putting pressure on Michael to halt the relationship. Soon enough, Michael is no longer in charge of Tactical Oversight, so he loses his office, and is no longer running missions. He's replaced by Davenport, a decent guy who's now in charge of field operations. Can Michael give up all the power he's earned in Section One for Nikita? And will Nikita let him give it all up, even if he wants to? Meanwhile, a sultry operative by the name of Valerie is putting heavy moves on both Walter and Birkoff, which soon enough puts a strain on their friendship.
After Birkoff chokes in the middle of remotely directing an operation and is then promptly upstaged by arch-nemesis Greg Hillinger who pulls the frying pan out of the fire and saves the mission, Operations promotes Hillinger to Birkoff's job and re-assigns Birkoff to his first field operation. Birkoff's mission is to infiltrate and perform reconnaissance on a mercenary terrorist organization "Soldat de la Liberty" run by a man named Jean-Marc Rousseau who employs brainwashing on young people to fill the ranks of his organization. Birkoff is convinced that Operation's real objective is to set him up with an impossible mission, so that Operations can eliminate Birkoff and permanently replace him with the more obsequious and pliable Hillinger. And sure enough, once inside the group Birkoff discovers ties between Rousseau's organization and the infamous Red Cell, and Operations refuses to extricate Birkoff preferring to leave him in place to gather more information. Can Nikita help Birko
During an operation, Hillinger's goofing off costs an operative his life, and Hillinger pleads with Birkoff to cover for him, which Birkoff inexplicably does. Hillinger doesn't return the favor, however, when Birkoff is sent out to direct a mission from the field, and Hillinger deliberately tries to get his rival Birkoff killed off once and for all. The jokes on Hillinger when Birkoff exposes what Hillinger did. Sure enough, Operations puts him in abeyance and Hillinger's days seem to be numbered. At the same time, Operations is acting more and more viciously toward Madeline. Operations' timing is terrible, as George from Oversight is turning up the pressure on Operations, just as he's acting out with Madeline. Will Madeline get even with Operations by betraying him to George?
Literally playing with fire, Michael and Nikita are setting up clandestine rendezvous on Section missions as a way to get around Operations and Madeline's ban on their seeing each other (See Third Party Ripoff). Operations and Madeline still suspect Michael and Nikita of seeing each other on the side, so Madeline starts sending Davenport along on Michael's and Nikita's mission to spy on them. Meanwhile, Madeline orders Birkoff to sweep Michael's and Nikita's computer panels for secret communication, and when Birkoff does indeed discover communications between the two, it implicates Walter as their go-between. Will Birkoff turn in Walter? And, if so, what will happen to Michael, Nikita and Walter?
Michael and Nikita are sent on an operation to find out who a pharmaceutical plant owned by a company named Genefex and a supplier of Red Cell who is selling a biological weapon named Gandium, too. Unbeknownst to Michael and Nikita, the operation has a secondary objective, to end Michael and Nikita's love affair once and for all. Once the mission objective is achieved, Nikita is sent to another part of plant, where Madeline is waiting to ""reprogram"" Nikita to eliminate her feelings for Michael. Meanwhile, Operations finally does the unthinkable, he sends Walter to ""retirement."" Birkoff has other ideas, and he immediately sets about sabotaging Walter's replacement, a young and innocent chap by the name of Giles.