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.

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.

Michael's son, Adam is a hostage of The Collective. Michael must save his son in a trade proposed by The Collective. Meanwhile, Haled is confronted by Michael on an offer to get rid of Graff, then leading Haled to become the head employee. Nikita & Michael do so, but this isn't good because Haled isn't alive anymore. This doesn't look too good for Michael. Two new candidates, Myra Mauk & Kelley are hoping for a spot at Section. Walter didn't have the best history with Myra, so he asks Jason Crawford to take her out of the running, he does so. More trades are offered later in the episode. Nikita is now running Section One, she lets Michael go to spend time with his son. Nikita says good-bye to Michael & continues are duties at Section One.

While Nikita is reassigned to Special Operative Jurgen, Section is contacted by one of Freedom League's operatives in order to verify Nikita's story about her capture.

Section believes that terrorists are after the nuclear power source of a downed satellite. They later discover the terrorists are actually after it because it is a military satellite and it will give them access to the Pentagon if they are able to salvage it and crack the codes. Nikita grows closer to Jurgen and Section uses it to their advantage.

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.

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?

When Nikita fails to assassinate Grenet, a Red Cell agent, and is unknowingly injured, Michael goes to her apartment to have dinner. It ends in disaster, when his water is poisoned and Nikita hands him over to Red Cell in exchange for his cornia files. She deletes herself from Section's databases and escapes to where they can't find her.

The situation is dire as The Collective, still led by Graff and Haled, is cleaning Section's clock. But, just in time, Michael asks Nikita to help him return to Section, where his re-emergence is viewed with suspicion by both Mr. Jones and Operations. While new missions continue against The Collective with Michael's return, Nikita admits that she lied to him in "Four Light Years Further," and that she does indeed love him. Operations discovers that The Collective has infiltrated Section's mainframe to try to locate and kidnap Michael's son Adam, in attempt to re-assert control over him. Can Operations foil The Collective's plans?

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.

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.

Nikita continues to show evidence of the "reprogramming," including ordering the elimination of a captured Section operative and endangering the lives of children during a mission, and taking part in the beatings of a captive. Michael is determined to reverse Nikita's reprogramming, and he soon determines that the former Section operative who came up with the "reprogramming" process, Ross Gelman, may be the key. Meanwhile, Operations couldn't be more proud of the "new" Nikita, but Madeline is still worried. Eventually, Operations concludes that Michael's attempts at restoring Nikita have gone too far, and takes extreme measures.

Michael kidnaps Nikita with Walter and Birkoff's help, and manages to reverse Gelman's process. Together, they outsmart Madeline and Operations leading them to return to Section.

After Substation three is destroyed by self-destruct, Section One investigates and finds a trace to Red Cell. What they also discover is that Red Cell has been taking similar blows. Operations decides to become allies and for each other to send top-notch agents. Operations sends Madeline, though Operations is willing to risk her.

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.

Nikita is brought back to full operative status when Birkoff discovers a six-man terrorist team are making several random attacks.

Egram Petrosian, the former Section deep cover agent rescued by Section One, takes over and promotes Nikita to second in command when Operations is seriously wounded by an insane operative.

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

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.

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.

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.

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

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?

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 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.