In season one of this sexy and suspenseful series featuring international action star Maggie Q in the title role, the charming and deadly Nikita waged a war against Division, the agency that created her. Michael - the man who trained her, a man she trusted - was hunting her. But Nikita had an ace up her sleeve: Alex, a girl she trained to infiltrate this secret unit of the government.
Nikita (Maggie Q) and Michael (Shane West) plot to take down Division and Oversight and are prepared to use the contents of the black box to do so. Amanda (Melinda Clarke) is now running Division but Oversight has assigned one of their own, a new agent named Sean (guest star) Dillon Casey), to keep an eye on her. Amanda’s first mission is to get back the black box from Nikita, and she enlists Alex’s help to do so. Alex refuses until Amanda tells her she will help her find the man who killed Alex’s father. Meanwhile, Nikita and Michael find help from an unlikely ally.
Mads visits Eduardo in the ICU and tells him she’s worried that her father may have had something to do with the accident in order to keep them apart.While investigating an old corrupt Division program, P9, that seems to have resurfaced, Nikita (Maggie Q) and Michael (Shane West) run into Owen (guest star Devon Sawa). He tells them he is searching for Dr. Joseph Mars (guest star John Ralston), who is not only the mastermind behind P9, but also invented the Regimen and could help Owen wean himself off the dangerous drug. Michael is hesitant to trust Owen again but Nikita decides the three should join forces. Percy (Xander Berkeley) demands to see Alex (Lyndsy Fonseca).
Birkoff (Aaron Stanford) tells Nikita (Maggie Q) and Michael (Shane West) that a black box file reveals that an international terrorist named Ramon (guest star Simon Kassianides), who has been taking credit for some serious political assassinations, now works for Division. This news upsets Nikita since she was the agent that captured Ramon years ago and turned him over to Percy (Xander Berkeley). Amanda (Melinda Clarke) convinces Alex (Lyndsy Fonseca) to kill Anton Kochenko (guest star Paul Braunstein), a man who used to work for Alex’s father, and plans to let Ramon take the credit for the murder. However, when Nikita disrupts Amanda’s plan, Amanda fights back by taking what Nikita loves most.
Nikita (Maggie Q) is stunned when she hears that her old Division partner Kelly (guest star Katheryn Winnick) escaped from a Turkish prison. Nikita thought Kelly died years ago and always felt responsible because it happened on the mission where Nikita escaped from Division. Knowing Amanda (Melinda Clarke) will go after Kelly, Nikita tells Michael (Shane West) they have to go to Turkey to help her. Amanda sends Alex (Lyndsy Fonseca) and Roan (guest star Rob Stewart) to Europe to stop the former partners from reuniting.
Michael (Shane West) discovers Cassandra (guest star Helena Mattsson), a woman he once romanced under Division orders, is in danger. Feeling guilty for how things ended, he wants to help her but Nikita (Maggie Q) suspects there is more to it than easing his conscience. Amanda (Melinda Clarke) manipulates Alex (Lyndsy Fonseca) into helping her on a mission but Sean (Dillon Casey) gets caught in Amanda’s web of lies and begins to doubt Division’s true motives.
While searching for information on the black box, Birkoff (Aaron Stanford) stumbles upon Nikita’s (Maggie Q) birth certificate. Nikita and Michael track down Nikita’s father Richard (guest star David Keith), but the reunion is not quite what Nikita expected. Percy (Xander Berkeley) tells Alex (Lyndsy Fonseca) that the black box that Nikita has contains information that could help her avenge her father’s death.
While in prison, Ryan (guest star Noah Bean) discovers patterns that reveal how Oversight gets its funding. Ryan arranges a meeting with Nikita (Maggie Q) to fill her in, but Amanda (Melinda Clarke) intercepts their coded messages to each other and alerts Oversight, who sends in one of their own to interrogate Ryan. Nikita and Michael (Shane West) scramble to break Noah out of prison before Oversight gets to him. Meanwhile, Alex (Lyndsy Fonseca) is being tailed by Gogol, and comes face to face with someone from her past.
Michael (Shane West) becomes alarmed when he hears Cassandra (guest star Helena Mattsson) is in trouble and rushes off to help her. He discovers General Tupelov (guest star Paulino Nunes) has accused her of stealing two million dollars and has threatened to kill her unless she returns it. However, when Cassandra’s story doesn’t add up, Nikita (Maggie Q) becomes suspicious of what she might be hiding. Meanwhile, Alex (Lyndsy Fonseca) receives a very tempting offer from Percy (Xander Berkeley) that could give her the resources to eliminate Semak.
Nikita (Maggie Q) steals funds from Oversight, forcing them to host an emergency meeting. Nikita and Birkoff (Aaron Stanford) figure out how to spy on the meeting so Nikita can identify the other members of Oversight, but things go awry and Sean (Dillon Casey) captures Birkoff. Amanda (Melinda Clarke) demands to know where Nikita is hiding but Birkoff refuses to give up his friend so she tortures him. Meanwhile, Alex (Lyndsy Fonseca) sets her plan in motion to reclaim her father's empire. With a price on her head, Alex realizes the easiest way to get into Russia undetected is the same way she was smuggled out – through the illegal sex ring.
With Michael (Shane West) out of town, Nikita (Maggie Q) turns to Owen (guest star Devon Sawa) to help her track down and steal another black box from a Guardian. Unfortunately, she discovers that Owen is working for an unlikely employer that could jeopardize Nikita's whole operation. Amanda (Melinda Clarke) realizes Alex (Lyndsy Fonseca) received privileged information about Semak (guest star Peter J. Lucas) and that information could only have come from Percy (Xander Berkeley). Furious that Percy undermined her, Amanda strips him of all his amenities. Back home in Russia, Alex finally makes her move on Semak.
Alex's mission to take down Gogol comes to a head as she infiltrates her childhood home and faces ghosts from her past. On a completely separate mission, Nikita also ends up at the mansion to steal Semak's (guest star Peter J. Lucas) black box. Nikita and Alex run into each other and decide to join forces, but they run into a major roadblock. Meanwhile, Michael and Owen (guest star Devon Sawa) work together to figure out Percy's secret plan with the Guardians.
Sean (Dillon Casey) attacks Nikita (Maggie Q) and Michael (Shane West) in an effort to protect his mother. Meanwhile, Percy (Xander Berkeley) gets the upper hand on Amanda (Melinda Clarke) and threatens to level Division unless she releases him.
Percy (Xander Berkeley) has his Guardians hold the members of Oversight hostage until Amanda (Melinda Clarke) agrees to his demands. If she doesn’t, the Guardians will shoot all the members of Oversight and release a deadly gas inside Division that will instantly kill everyone, including Amanda. Nikita (Maggie Q) is torn between letting the enemy fall and saving the innocent lives inside Division. Meanwhile, Sean (Dillon Casey) is frantic to save his mother from Percy’s clutches and turns to Nikita, Michael (Shane West) and Alex (Lyndsy Fonseca) for help.
Percy (Xander Berkeley) continues his plan to take back Division by threatening to kill Nikita’s (Maggie Q) mentor Carla (guest star Erica Gimpel, “Fame”), the woman who took Nikita off the streets when she was a junkie. Determined to get to Carla before Percy, Nikita uses Madeline (guest star Alberta Watson) to send her a message. Percy intercepts the message and it’s a race to see who can get to Carla first. Meanwhile, Amanda (Melinda Clarke) tells Alex (Lyndsy Fonseca) it’s time for her to take back Zetrov and reveal to the world that Alexandra Udinov is alive.
Nikita (Maggie Q) and Michael (Shane West) try to help Carla (guest star Erica Gimpel) remember her past, which holds the key to taking down Division. Carla recounts the night Nikita was arrested and Nikita is stunned at what she learns. Meanwhile, Alex (Lyndsy Fonseca) shows up at a Zetrov press conference where Semak (guest star Peter J. Lucas) is speaking and announces that she’s Alexandra Udinov. Alex demands a trade – her mother for the empire.
Division agents are assassinated one by one, and Amanda realizes that Percy is behind the murders. She reluctantly asks Nikita for help in exchange for Ryan.
Michael learns a secret that Cassandra kept from him, so he and Nikita travel to Moscow to confront her. Meanwhile, Alex makes one last attempt to find her mother by sending out a coded message through a TV interview.
Amanda and Ari set up a board meeting with Zetrov and prepare to take over the company, and Nikita recalls what Amanda was like when she was first brought to Division. Meanwhile, Alex surprises Ari by showing up at the board meeting with a powerful friend.
When Nikita (Maggie Q) worked for Division, she targeted a man named Nicholas Brandt (guest star Rick Ravanello) and infiltrated his inner circle. She captured him and he's been behind bars ever since. However, Percy (Xander Berkeley) springs Brant, and his first mission is to capture Nikita for payback. After he has her in his clutches, he tortures her, forcing Nikita to face a side of herself she thought she had long buried. Meanwhile, Percy continues to play mind games with Michael (Shane West), Alex (Lyndsy Fonseca) and Sean (Dillon Casey), pushing one of them to the brink of death.
Nikita (Maggie Q) convinces a reluctant Birkhoff (Aaron Stanford) to use 20 million dollars of his own money in a plan to bankrupt Percy (Xander Berkeley) and Division, but when Percy ends up stealing Birkhoff's entire life savings, Birkhoff and Nikita clash. Team Nikita has one last chance to hit Percy again, but Birkhoff is arrested trying to regain his millions and Nikita realizes she must break him out of jail before Division gets to him. Michael (Shane West) and Alex (Lyndsy Fonseca) go after Birkhoff’s stolen money while Nikita goes to save Birkhoff.
When it looks like Percy's (Xander Berkeley) nuclear weapons plan is getting out of control, Ryan (guest star Noah Bean) suggests they go to the Director of the CIA, Morgan Kendrick (guest star Brian Howe), for help. Nikita (Maggie Q) is vehemently opposed to the plan and is surprised when Michael (Shane West) takes Ryan's side. Tensions escalate when Nikita is proven right after they discover Kendrick has a link to Percy. Meanwhile, Sean (Dillon Casey) is shot by Percy's men, shaking Alex (Lyndsy Fonseca) to the core.
Percy (Xander Berkeley) calls the President the United States (guest star Cameron Daddo) and threatens to set off a nuclear explosion unless his demands are met. Birkhoff (Aaron Stanford) finds two scientists who could help stop Percy's new nuclear satellite, so Nikita (Maggie Q) and Michael (Shane West) head after one and Sean (Dillon Casey) and Alex (Lyndsy Fonseca) look for the other. Unfortunately, Alex and Sean get caught at the very location that Percy blows up as an example of his power. Meanwhile, Nikita realizes the best way to stop Percy is to go into the belly of the beast's Division itself.
Nikita (Maggie Q) and Michael (Shane West) invade Division in an attempt to capture Percy (Xander Berkeley). Alex (Lyndsy Fonseca) and Sean (Dillon Casey) get caught in a deadly gunfire battle with the U.S. Marines and Ryan (Noah Bean) must convince the President of the United States not to destroy Division until he is sure Nikita and Michael are safely out of the building, but the President is eager to end Percy's reign. Meanwhile, Birkhoff (Aaron Stanford) asks Sonya (guest star Lyndie Greenwood) for help, and Nikita corners Percy in his office, but he pulls out one final trick that may cost her the battle.