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.

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.

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.

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?

Michael discovers that Adrian's mind is not blank as he thought it is. Together they try to save George from Operations and Madeline's attempt to assassinate him. Meanwhile, Michael kidnaps Nikita in a futile effort to reason with her.

The unbelievable happens! Nikita is called before Operations and Madeline and is given fantastic news, she's free! As part of a ""pilot program,"" Nikita is granted her freedom and a normal life, as long as she never contacts anyone from Section again, and as long as she agrees to be regularly evaluated. Nikita is skeptical at first, but after 6 weeks on ""the outside,"" she starts to believe that maybe this is for-real. Sure enough, George from Oversight shows up with the strings, in exchange for her freedom, Nikita must do one thing, return to Section One to kill Operations! The man whom George claims killed Nikita's real father. Will Nikita do it?

Another incursion takes place in Section One, this time in the form of a virus that is making Section One's members sick, one by one. Taking matters into his own hands, George orders in his own Bio Team to treat Section's members. Operations suspects George has an ulterior motive. Sure enough, when Section's people, starting with Walter, followed by Nikita, go in for their ""examination"" with George's Bio Team, they come out vegetables. It seems George's team is mind wiping (downloading the contents of the brains) the Section's members. This process causes them to relive their lives, before leaving them vegetables. Can Michael and Birkoff stop George's team before everyone in Section One gets their brain sucked?

Birkoff may have stumbled on Section One's biggest coups yet, a chance to nab a top Red Cell operative by the name of "The Cardinal", who has eluded Section One for more than 15 years. Unfortunately, Birkoff's arch-nemesis Greg Hillinger is convinced that Birkoff is wrong, and Hillinger convinces George that Operations and Section One are walking into a trap. Based on Hillinger's intellect, George moves against Operations on the assumption that the operation against The Cardinal is bogus. Is Birkoff right after all? And if Birkoff is wrong, is this the end of Operations, and Birkoff too?

Michael escapes Red Cell and is assigned to meet Nikita and kill her, however she doesn't show up and an Alpha Team is assigned to track her down. Michael leads the team with Kate Quinn. Before the mission, Michael discovers Quinn is Nikita and that he could leave Section. The Alpha Team is wiped out and Michael escapes with Nikita.