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.

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 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 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.

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.

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.

Ryan takes charge of Division with Nikita by his side. Their first mission under the new regime is to bring in “The Dirty Thirty,” the rogue agents who failed to respond to the Division recall after Percy was killed. Unfortunately, their first mission doesn’t go as planned and Michael is arrested, forcing Nikita to change gears and hatch an escape plan for him. Alex reprises her alter ego, the spoiled Russian princess Alexandra Udinov, in a very unique way as part of the plan to spring Michael. Meanwhile, Birkhoff struggles to maintain a working relationship with Sonya, despite his growing attraction to her.

Nikita, Michael and team extract a young girl named Liza, who is being held captive by a rogue Division agent, Wade. Wade has brainwashed Liza and trained her to be a Division agent to help him on his own personal mission. Nikita tries desperately to break through to Liza but, in a moment of chaos, the girl escapes Division. The team races to find her before she can complete her mission to unleash a deadly chemical into the UN building during a special event. Meanwhile, Liza’s abduction brings up painful old memories for Alex.

When Ryan tells Nikita an undercover agent has been arrested and they need to extract her from prison, Nikita questions why Division is continuing to run Percy’s old missions. Nikita, Michael and Sean attempt to stop a terrorist attack but are one man down after Alex is shot. Meanwhile, Birkhoff and Sonia continue to bicker.

Amanda sends a rogue Division agent, Anne to spring Owen from a Russian prison, but Owen manages to escape her clutches and sends a message to Nikita that he’s free. When Nikita tracks him down, Owen is shocked to learn that Nikita is with Division now but returns to base with her. Michael and Ryan aren’t sure they can trust Owen but Nikita stands by her friend.

When a former undercover Division agent, Markov, is elected President of Uzbekistan, Nikita and her team decide to capture him during his visit to the United States.

Nikita and Michael capture Cyrus, an arms dealer, who is purchasing a weapon-jamming device for Ari. Nikita convinces Ryan to let them use Cyrus as bait to capture Amanda but Cyrus manages to escape the trap. However, when Amanda double crosses Cyrus, his only hope for survival is Nikita. Meanwhile, Birkhoff is hot on the trail of Amanda’s mole and Alex starts to unravel.

Birkhoff tells Nikita that Sonya is Amanda’s mole and not only has Amanda reactivated Sonya’s kill chip but she also placed a second mole in Division to keep an eye on her. Nikita, Michael and Ryan devise a plan to use Sonya to ferret out Amanda’s hiding place and Birkhoff sets a trap for the second mole. Meanwhile, Michael confronts Alex about her drug use and she begs him not to tell Nikita.

Nikita and Owen face off against a rogue “cleaner” named Liam, while Michael takes a new position at Division. Michael and Nikita’s relationship becomes strained as he watches her work with Owen.

A CIA agent named Naomi comes across a file detailing Madeline Pierce’s involvement with Division and turns it over to the Director of the CIA, Morgan Kendrick. When Kendrick is killed shortly thereafter, Amanda frames Sean for the assassination and the CIA takes him into custody. Nikita promises Alex they will free Sean and comes up with a plan that could either save him or cost him his life.

Amanda holds Alex hostage and tells Nikita she will release Alex in exchange for Ari. Michael assigns Nikita and Sean to handle the exchange of prisoners, but Ryan adds Owen to the team at the last minute, which makes Michael suspicious. While in captivity, Alex befriends a fellow prisoner named Larissa and vows to break them both out of the jail, which ultimately conflicts with Nikita’s plan, forcing Alex to choose between Nikita and her promise to Larissa.

When Nikita decides Division should take on a government mission to eliminate the President of Chad while he’s in Paris, Alex takes a stand and refuses to participate. Upset that Nikita is keeping secrets from everyone, much like Percy did, Alex recruits Birkoff to dig up secrets on Danforth to use as leverage in case things get messy with the government. Alex and Birkhoff are shocked when they come across a secret so big it could blow up Division — literally.

Nikita and Michael learn of a new prosthetic hand that could have Michael back to his old self, but it comes at a steep price. Meanwhile, Alex and Sean are tasked with investigating who, inside Division, is behind a mutiny that ends in bloodshed.

Alex confesses her desire to leave Division to Birkhoff, while Amanda begins providing Owen with something he was never able to find – memories of his real past. Despite Nikita’s attempts to help, Owen begins to confront the events of his past.

Strapped down and drugged, Nikita is subjected to Amanda's horrific mental conditioning process, sending her down a terrible trip through memory lane. In the process, Nikita discovers Amanda's deepest, most guarded secret ever. Now revealed as leader of the uprising, Alex struggles to save everyone as events violently escalate. With Michael locked away by Division conspirators, Birkhoff and Sean must step up to save the women they love. Meanwhile, Owen's newfound memories drive him to disturbing actions during Division's lockdown.

Shattered by Amanda’s programming, her inability to save everyone, and her ultimate responsibility for the tragic events at Division, Alex reverts to old ways and violently strikes out. With most of their compatriots dead, broken, or scattered to the wind, Nikita and Michael together must pick through the ashes of Division to see who and what can be salvaged – and quickly, before the President realizes the sinking depth of the damage. Memories of Division’s glory days haunt them. Birkhoff struggles with his own personal losses.

Seized from the wreckage of Division, the black box falls into the hands of a mutinous agent guided by Amanda. Select leaks to sweeten the box's sale immediately put what's left of the team in peril from potential international buyers and the President. With no support staff, few leads, and clock ticking, arms dealer/reformed rogue Cyrus returns to do right. With his help, Nikita, Michael and Alex stage a daring op at the tightly-secured G-20 economic summit to regain control of the box and everyone's future.

Before becoming engaged, Nikita said, "There's always gonna be another mission." Now, after barely surviving harrowing recent events, Michael questions his fiance's commitment to a life beyond Division's web of deceit, double-crosses and murder - and he's not the only one with doubts. Still, the remaining threat of Amanda looms large over the team, particularly since she's now allied herself with mysterious new partners that furnish her with a terrifying new weapon. Meanwhile, Alex considers an intriguing offer from the Nobel Prize winner she's defending.

Amanda forces Nikita into a life-threatening situation where she has to choose between saving Michael or saving herself. The team races to find a way to stop Amanda, but with a diminished Division, they might finally be out-gunned.

Nikita is still on the run after she was framed for the assassination of the President of the United States. Dale, a reporter from the news channel ENN, starts questioning what really happened that night. Nikita sees this as an opportunity to clear her name so she re-enters the country to talk to Dale but walks right into a trap set by Amanda. The team is alerted and Michael sets out to find Nikita before Amanda does. While Birkoff and Ryan help Michael from their new mobile office, a high-tech aircraft, Alex stakes out a human-trafficking ring and learns The Shop is involved. Things go south and Alex is surprised when Owen/Sam shows up at the scene.

Nikita reunites with Michael, Birkhoff and Ryan aboard the team’s aircraft command center. Michael refuses to discuss their relationship but tells Nikita she should stay with the group and let them help her clear her name. Ryan realizes Amanda is making doubles of VIPs with The Shop’s help. Nikita discovers that one of the doubles is the Director of the FBI, but doesn’t know how to kill him without exposing herself. Meanwhile, Alex holds Sam at gunpoint and demands he return what he stole from her, but when a gang of thugs attacks them they are forced to work together to escape.

Tensions continue to escalate between the United States and Pakistan after Amanda plants evidence that Pakistan hired Nikita to kill the President. Ryan becomes suspicious of Birkhoff's increasingly odd behavior and tells Nikita and Michael that he thinks Amanda may have kidnapped Birkhoff and planted a double on the plane. Meanwhile, the CIA captures Alex and questions her about her involvement with Nikita.

Just as Nikita is finally starting to see an end to the long war with The Shop, Ryan confesses a secret that could unravel it all. Meanwhile, Michael tries to get Nikita to accept their new circumstances as he contemplates what comes next for the two of them. Realizing Sam was planning to steal her diamonds, Alex gives him a suitcase of fake diamonds to deliver to her contact in France. Alex is surprised when he upholds his end of the bargain and doesn’t take off with the jewels. However, things get messy when Sam is jumped by the loan shark he owes money to, and Alex must step in to save him.