Nikita waged a war against Division. In the process, her relationship with Alex, the girl she trained to infiltrate the secret agency was destroyed, and her relationship with Michael, the man who trained her, was restored. Now, Nikita and Michael are on the run with a hard drive containing the government's darkest secrets and conspiracies. Together, they are going to right the wrongs that Division has committed over the years, one mission at a time. But leading the hunt for them this time is Alex...and she knows all of Nikita's tricks.
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. Percy demands to see Alex.
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 stumbles upon Nikita’s birth certificate. Nikita and Michael track down Nikita’s father Richard, but the reunion is not quite what Nikita expected. Percy tells Alex that the black box that Nikita has contains information that could help her avenge her father’s death.
While in prison, Ryan discovers patterns that reveal how Oversight gets its funding. Ryan arranges a meeting with Nikita to fill her in, but Amanda intercepts their coded messages to each other and alerts Oversight, who sends in one of their own to interrogate Ryan. Nikita and Michael scramble to break Noah out of prison before Oversight gets to him. Meanwhile, Alex 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 hundred 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.
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 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 work together to figure out Percy’s secret plan with the Guardians.
Sean attacks Nikita and Michael in an effort to protect his mother. Meanwhile, Percy gets the upper hand on Amanda and threatens to level Division unless she releases him.
Percy has his Guardians hold the members of Oversight hostage until Amanda 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 is torn between letting the enemy fall and saving the innocent lives inside Division. Meanwhile, Sean is frantic to save his mother from Percy's clutches and turns to Nikita, Michael and Alex for help.
Percy continues his plan to take back Division by threatening to kill Nikita’s mentor Carla, the woman who took Nikita off the streets when she was a junkie. Determined to get to Carla before Percy, Nikita uses Madeline to send her a message. Percy intercepts the message and it’s a race to see who can get to Carla first. Meanwhile, Amanda tells Alex it’s time for her to take back Zetrov and reveal to the world that Alexandra Udinov is alive.
Nikita and Michael try to help Carla 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 shows up at a Zetrov press conference where Semak is speaking and announces that she’s Alexandra Udinov. Alex demands a trade – her mother for the empire.
Division is in an uproar when their agents are being assassinated one by one. Amanda realizes Percy is behind the murders and is trying to undermine her authority with the other Division agents. She reluctantly calls Nikita with an offer that is hard to resist – stop Percy and she’ll give Nikita Ryan.
Michael is furious when he discovers a secret that Cassandra kept from him, so he and Nikita fly to Moscow to confront her. Meanwhile, Alex makes a last ditch effort to find her mother by sending out a coded message through a televised interview.
Amanda and Ari set up a board meeting with Zetrov and prepare to take over the company. After a heated face-to-face confrontation between Nikita and Amanda, 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 an old and powerful friend.
When Nikita worked for Division, she targeted a man named Nicholas Brandt and infiltrated his inner circle. She captured him and he’s been behind bars ever since. However, Percy 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, Alex and Sean, pushing one of them to the brink of death.
Nikita convinces a reluctant Birkhoff to use 20 million dollars of his own money in a plan to bankrupt Percy 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 and Alex go after Birkhoff’s stolen money while Nikita goes to save Birkhoff.
When it looks like Percy’s nuclear weapons plan is getting out of control, Ryan suggests they go to the Director of the CIA, Morgan Kendrick, for help. Nikita is vehemently opposed to the plan and is surprised when Michael takes Ryan’s side. Tensions escalate when Nikita is proven right after they discover Kendrick has a link to Percy. Meanwhile, Sean is shot by Percy’s men, shaking Alex to the core.
Percy calls the President the United States and threatens to set off a nuclear explosion unless his demands are met. Birkhoff finds two scientists who could help stop Percy’s new nuclear satellite, so Nikita and Michael head after one and Sean and Alex 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 – Division itself.
Nikita and Michael invade Division in an attempt to capture Percy. Alex and Sean get caught in a deadly gunfire battle with the U.S. Marines and Ryan 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 asks Sonya for help, and Nikita corners Percy in his office, but he pulls out one final trick that may cost her the battle.