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.

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.

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.

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?

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.

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 Michael eludes Operations' first cancellation attempt, Operations puts all missions on hold and sends out a team to kill him. Michael again manages to escape certain death, but this time he returns to infiltrate Section. Determined to find the files that possess the formula for deprogramming Nikita, Michael is stunned to discover who Section's first test subject was; Adrian, Section One's founder, whose effort to topple Operations failed two years earlier. To gain leverage against Operations, Michael kidnaps Adrian, but her help proves limited when Michael discovers her mind is gone.

Michael and Nikita have been traveling from place to place, keeping one step ahead of Section One's attempts to find them. When George is eliminated from the picture after leaking intel to Red Cell in order to discredit Section One, the newly-empowered Operations and Madeline finally track down Michael and Nikita. They bring them back to Section. Just as Michael and Nikita are about to be cancelled, all of Section's systems suddenly stop. Mr. Jones, the mysterious head of Center, is on his way to Section One in order to conduct an evaluation, and has put Section in stasis. When Jones arrives, he is really Nick Shtoppel Nikita's neighbor and Section informant. He reveals that Nikita has been secretly working for Center for the last three years. Nikita assists Jones with his evaluation, and things change radically. Operations is forced to remain at Section One for the next seven years. Madeline takes her own life rather than be cancelled. Walter is transferred to the Farm, where he will

Section One is hot on the trail of Tyler, one of the world's most dangerous terrorists. After Tyler kidnaps a young inventor who has created a new, completely un-detectable plastic explosive, Nikita is sent to try and rescue the inventor and keep his knowledge out of Tyler's hands. When the mission is unsuccessful, Nikita is given orders to cancel the inventor, but she refuses. Operations decides that Nikita has crossed the line, and he purposely sends her on a suicide mission to destroy a terrorist hideout. Michael intervenes and gives Nikita the means to escape, but her freedom will change both of their lives forever.

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.

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.