Section One's computer security is breached and the directory of all their agents is stolen. Michael goes to Prague to reclaim the directory, but the man who stole it is killed by another terrorist seeking the directory for himself. Nikita discovers that it was randomly left with a civilian passenger on a Prague city bus, architect Gray Wellman. Nikita is assigned to Gray in order to get close to him and retrieve the directory, but when she starts falling for him, her actions not only threaten the mission, but Section One's very existence.

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.

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.

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.

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?

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?

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.

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.

Seeking a lost command clone (a computer-like device that apparently allows the user to command a Section without outside aide) that was apparently captured by Red Cell and then stolen by another terrorist group, George and Oversight orders Section one to work together with an agent from Section Four to search for the missing ""command clone."" What is Section Four? Apparently, it's the Section where people/agents with extrasensory abilities are developed. So, who is the agent from Section Four? None other than a 12-year old boy by the name of Gerome. Of course, with his extrasensory abilities, Gerome soon overwhelms the ability of Madeline and Operations to control him. Can Nikita bring Gerome under control before he destroys Section One?

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.