With Michael's help, Nikita survived the destruction of a Freedom League hideout in the first season's final episode. Since then, she has been on the run from Section One. While working as a waitress, Nikita is captured by the Freedom League and used as bait to lure Section One into a trap. During a raid by a Section team led by Michael, Nikita saves Michael's life and they manage to escape together. Later, on an abandoned ship, Nikita and Michael share a night of passion. However, Michael's lies about Nikita's whereabouts are in danger of being exposed.

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.

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

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.

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.

During a mission, Michael is forced into a stage where he must cut communication with Section and complete the mission at any cost, but the target of Michael captures Madeline, and Operations is willing to kill Michael in order to protect her.

Michael's loyalties are divided when Nikita discovers his friend is a bomber and Operations tells him to betray his friend.

Nikita and Michael are sent on a mission to take out someone in a Balkan nation, but Nikita must force Michael into protecting two displaced children, however that protection prevents Nikita from hitting their target, and they must risk their lives in order to get him down.

On an assignment to capture a Red Cell agent known as Jenna, with valuable information, Nikita is arrested and brought to jail in order to serve time, where Jenna is also serving time. But she is forced to betray the trust she has with Jenna when she must escape the jail along with her, only for Jenna to be captured and interrogated.

Nikita is promoted to team leader early and is sent on a much more dangerous than expected mission with a disobedient operative.

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 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.

Michael is captured and interrogated by terrorists, then loses his memory and does not know who he is.

Michael and Nikita are sent on a mission along with former hit man David Fanning, but during the mission he takes Nikita hostage and demands that Michael return his wife, or Nikita will be killed.

Section captures a mathematician in order to decode a code that is aiding terrorists in their attacks.

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

A new recruit named Andrea is romanced by Michael. When she learns that it was just a setup to gain allegiance to Section, she wants Nikita's help for revenge. Upon Nikita's refusal, Andrea proves dangerous to both Nikita and Michael when their mission ends up in a dangerous lab containing viruses.

Operations orders a raid to capture the leader of a terrorist group, which turns out to be a sentient computer.

When Section discovers a wealthy terrorist plans to fund upcoming civilian attacks, Michael and Nikita pose as money launderers in order to stop him. However, his assistant, Giraldi, claims to be a Section operative who has been in the field for nine years and wants to be brought back in. When Nikita informs Operations, he tells her to ignore his request, but when Madeline finds out, she insists Nikita bring him in. Now, Nikita is caught between Madeline and Operations, and a man's life hangs in the balance.

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.

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.