A street girl is wrongly imprisoned for murder, but she is offered an escape clause by a covert governmental agency who want to employ her as an assassin.
While meeting a contact, Nikita is recognized by an old friend - dating to before he entered Section. When Nikita reports to the contact, she worries about what Operations will do.
Nikita poses as a recruit to a terrorist group... only to learn that the group has had a Section agent prisoner for years - someone who is very important to Michael.
Nikita is ordered to romance a man that Section believes to be laundering money for terrorist organizations.
Nikita poses as the long-lost daughter of a woman, who with her husband is attempting to sell a nuclear trigger.
Nikita and Michael pose as guns for hire to infiltrate an arms dealer's organization and prevent a biological attack.
When a Section operation fails, Nikita begins to suspect that someone inside Section may be tipping off their target.
Nikita is approached by another member of Section - leave, and escape with him. But Nikita can't decide if it's merely a test by Section, and her feelings for Michael also complicate the matter.
A Section database is stolen, and Nikita is assigned to help recover it. But the mission becomes complicated for her when her feelings for the man she's assigned to get close to start to become real.
Six months have passed since Michael engineered Nikita's escape from Section, during which time he's heard no word from her; and causing his performance to degrade. And after six months of being on the outside, Nikita is captured by Freedom League, causing her to wonder if the only freedom she can have is by returning to Section.
Nikita suddenly comes back to Section after disappearing for 6 months, saying that she was held captive by the terrorist Freedom League all this time. Operations is suspicious and asks an operative named Jurgen to do her retraining while surreptitiously checking out her story. Michael is worried because he knows Nikita is lying.
Nikita is approved to return to active service; but reports now to Jurgen instead of Michael. Jurgen's obvious interest in her, combined with Michael's coldness, puts Nikita in the middle of two very dangerous men. Meanwhile, Section is on the trail of new terrorist group known as Helix.
As Nikita's relationship with Jurgen develops, there are signs that not all is well inside Section. Meanwhile the team is on the hunt for a satellite that crashed due to a launch failure.
Operations is shot by one of his own operatives, and Egran Petrosian returns to take over Section - choosing Nikita as his second-in-command.
When Michael's communication with Section during a mission is compromised, resulting in mission failure, Michael is forced to adopt the "Mandatory Refusal" protocol. Now he must complete the mission on his own, even though Section now wants the mission canceled, and mobilizes their agents to stop Michael.
When Nikita and Michael discover a bomb at a local park, Michael discovers that someone from his past is back.
Nikita and Michael are sent into a war-torn Bosnia-type country to stop an arms deal from taking place; however, the mission is complicated when Nikita takes two refugee children under her protection.
A Red Cell operative, who possesses crucial intelligence on a Red Cell mission, is being held in prison in a hostile country. Nikita must enter the prison, and then escape with the operative.
Nikita is made a team leader for the first time. Now she must plan and execute a mission, as well as deal with a troublesome team member.
Nikita poses as a psychic to gain access to head of a terrorist organization - a man who wants her to get in contact with his dead son.
Working to take down a rogue intelligence agent, Nikita learns that a member of her team has a secret - a secret that both jeopardizes her teammates performance, and possibly the mission. Nikita has already been warned by Operations that her unorthodox methods must come to an end; once again putting Nikita in the position of hiding information from Section.
During a mission, Michael is captured and injured while under interrogation before they can get him out. Nikita, fearing that Michael could be canceled if Operations learns of his disability, tries to hide this information from Section.
David Fanning, an assassin that Michael and Nikita captured during a prior op has been recruited to Section; and assigned to work a mission with them. Things go wrong during the mission, and Michael is forced to contact Lisa, Fanning's wife.
Unable to crack an enemy code, Birkoff suggests that they co-opt the services of someone outside of Section One - a genius in the field who also still happens to be a teenager.
In order to gain intel on a group known as Bright Star, Nikita makes contact with a forger, named Formits, who works for them. But during the assignment, Nikita learns that Formits has his own dark side - pitting her inherent sense of right and wrong, against Section's goals.
A deadly bacteria is released into Section, and it's up to Nikita and Michael to track down the designer and obtain an antidote.
After a mission goes wrong, Michael blames the mission profiler, Andrea Kosov. Operations assigns her to Michael's team to get some real field experience. Andrea turns out to be the opposite of Nikita - someone who likes their job, and life in Section.
During a mission to take out a maned code-named Brutus, that has been intercepting Section communications, Nikita and Michael instead find an empty building - with only a sophisticated computer in place.
While on an operation to infiltrate the organization of Abel Goldner, a man known to fund rebel leaders, NIkita is approached by the Golner's aide - who claims to know about Section.
Nikita is contacted by a woman named Adrian, who claims to be the founder of Section. Adrian claims that Operations, and Section, are out of control, and must be taken down. Nikita must decide whether to join Adrian's cause.
In the season 2 finale, Adrian dispatches Nikita to retrieve a file code-named Gemstone. Gemstone, according to Adrian, will give them the proof to take down Operations and Section.
Michael is seen meeting enemy agents, and proceeds to wreak havoc at Section One by drugging Operations. As confusion reigns, he leads former lover Nikita into a deadly trap and attempts to form a partnership with terrorist group Red Cell.
Michael and Nikita are assigned a personal mission to rescue war veteran Willie Kane, who has fallen on hard times since being hailed a hero for saving Operations from death in Vietnam.
The government assassin is recruited to join a pilot programme which allows her to leave Section One - but fears it is because she knows so much she needs to be killed.
A virus begins infecting Section One's members, prompting George from Oversight to order his own bio team to administer treatment - but unfortunately their efforts erase Walter and Nikita's memories, turning them into virtual vegetables.
Section One recruit a boy with telekinetic powers to retrieve a stolen package, but have trouble ensuring his paranormal abilities are kept under their control.
Michael and Nikita are assigned to train five new recruits to combat terrorist group Crystal Sky, but find their students particularly hostile.
Nikita comes face to face with the true leader of the Centre - none other than her own father.
Nikita's relationship with Mr. Jones puts her in deadly danger as Operations takes drastic measures to secure his own position in the hierarchy. Having survived an attempt on her life, Nikita puts her job on the line to find her arch-enemy before the Collective get hold of him.
Operations discovers the Collective has infiltrated Section's mainframe in a bid to locate and kidnap Michael's son Adam. The agent asks Nikita for help returning to Section One - but Jones is suspicious of his intentions.
Michael insinuates his way into Section One, where he promptly tries to kidnap Mr Jones and hand him over to the Collective in return for his son - forcing Nikita to make a terrible choice.