Now an agent, Alex gets a new apartment and is given a cover job. She meets her new neighbor Nathan who invites her to a party at his house. Nikita warns Alex about getting too involved with people but Alex struggles between her duties at Division and living a normal life. Nikita realizes Division has implanted a kill chip in Alex's head and sets out to gain control of the chip. While interrogating Birkhoff, Nikita stuns Ryan by revealing a secret.
Alex's first assignment is a group mission to kill the Prince of Georgia at a museum gala. After Alex tells Nikita about the order, the two devise a plan to foil the assassination. However, Nikita trusts the wrong person and their plans are foiled, resulting in a stand-off and alerting Division that Nikita is in the building. Percy sends Michael in to kill Nikita.
Ryan intercepts a message about a dangerous cutting edge weapon coming into the U.S. so he asks Nikita to help him stop the delivery. Nikita discovers the man bringing the weapon into the country is Voss, a man she was forced to have a relationship with while undercover at Division. She reluctantly resumes her alter ego to retrieve the missile. Meanwhile, Michael interferes in Alex's new life with Nathan
While out on a mission for Division, Alex runs into Irina, a woman from her past. Alex tries to help Irina break free from her captor, but her old friend double crosses her and turns Alex over to Vlad, a Russian mobster, with a debt to settle. Nikita realizes Alex is in trouble and sets out to save her but runs into Michael who is searching for his missing agent. Realizing she can't compromise Alex's secret, Nikita must find a way to work with Michael to save Alex without getting her friend killed by Division.
In order to speed up her healing, Amanda sedates Alex after her last mission then takes advantage of Alex's drugged condition to question her about the secrets Amanda believes Alex is keeping. Nikita realizes Alex is in danger and tries to secure her another identity to smuggle her out of the country. However, Nikita's contact double-crosses her and she comes face to face with a surprising opponent. Meanwhile, Michael becomes suspicious of Alex and asks Birkhoff to investigate her.
Michael confronts Nikita in her lair and reveals that he knows Alex is the mole. He tells Nikita that she has 24 hours to find Kasim, the man who killed Michael's family, or he will tell Percy about Alex.
Owen returns with information on one of Percy's black boxes. Nikita returns to London with him to retrieve it but notices that Owen is acting strangely. Owen tells Nikita that he wants to release the contents of the black box and when Nikita disagrees, he turns on her. Meanwhile, Percy finds out Nikita is in London and dispenses Michael to kill her. Also, Amanda overhears Jaden arguing with Alex about the escape tunnels so she hooks Alex up to a lie detector to get the truth out of her once and for all.
Nikita believes it's getting too dangerous for Alex at Division and decides its time Alex disappeared. Alex agrees but before the plan can be put in motion, she and Jaden are assigned to an overseas mission to stop the son of a foreign president from selling a newly developed nerve toxin. Things go awry and Alex must decide between saving the mission or saving herself.
Frustrated that Nikita continues to intercept his black boxes, Percy sends Michael to check on one of the boxes and the guardian attached to it. Nikita makes it to the small Pennsylvania town first and is shocked to find that the guardian is a normal woman named Dana who has abandoned her post and is attempting to live a normal life with her husband and child. Tensions mount when Michael is forced to report Dana's actions and Division swarms in to clean up any evidence of her existence. Meanwhile, Alex and Jaden get into an argument and Nathan gets caught in the ...
After Michael learns that Percy has ordered Divison to kill anyone who could decrypt the black boxes, he sends Nikita in to save the last person on the list, a CIA cryptographer named Malcolm. Nikita kidnaps Malcolm and takes him to Ryan for protection. Meanwhile, Percy turns on Alex.
Nikita and Michael plot to take down Division and Oversight and are prepared to use the contents of the black box to do so. Amanda is now running Division but Oversight has assigned one of their own, a new agent named Sean, 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.
While investigating an old corrupt Division program, P9, that seems to have resurfaced, Nikita and Michael run into Owen. He tells them he is searching for Dr. Joseph Mars, 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.
Birkoff tells Nikita and Michael that a black box file reveals that an international terrorist named Ramon, 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. Amanda convinces Alex to kill Anton Kochenko, 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 is stunned when she hears that her old Division partner Kelly 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 will go after Kelly, Nikita tells Michael they have to go to Turkey to help her. Amanda sends Alex and Roan to Europe to stop the former partners from reuniting.
Michael discovers Cassandra, a woman he once romanced under Division orders, is in danger. Feeling guilty for how things ended, he wants to help her but Nikita suspects there is more to it than easing his conscience. Amanda manipulates Alex into helping her on a mission but Sean 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 Ryan 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 becomes alarmed when he hears Cassandra is in trouble and rushes off to help her. He discovers General Tupelov 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 becomes suspicious of what she might be hiding. Meanwhile, Alex receives a very tempting offer from Percy that could give her the resources to eliminate Semak.
Nikita steals funds from Oversight, forcing them to host an emergency meeting. Nikita and Birkoff figure out how to spy on the meeting so Nikita can identify the other members of Oversight, but things go awry and Sean captures Birkoff. Amanda demands to know where Nikita is hiding but Birkoff refuses to give up his friend so she tortures him. Meanwhile, Alex 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 out of town, Nikita turns to Owen 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 realizes Alex received privileged information about Semak and that information could only have come from Percy. Furious that Percy undermined her, Amanda strips him of all his amenities. Back home in Russia, Alex finally makes her move on Semak.