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.

Frustrated that MDK is still active, Nikita decides to end it her way. Leaving Michael and the team behind, Nikita takes Alex on the road to exact revenge. Nikita and Alex capture Mr. Jones and force him to reveal the names of the rest of the members of MDK. Armed with the information, Nikita goes down a dark path that may ultimately cost her her soul. Michael tracks her down and must get her to surrender before the military opens fire and kills her. However, Nikita isn't one to give up on a fight, leading her to make a shocking decision.

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.

Jones benches Amanda and takes back the reigns of the operation. He calls Nikita and offers her and the entire team complete freedom by wiping away their identities and faking their deaths if they walk away from their mission. The team lands the plane on a secluded Pakistan air strip, but when the local drug czar and his men storm the plane and demand ten million dollars, so Nikita calls Alex for the money. After Alex pulls diamonds out of a safe deposit box to pay the insurgents, Sam sees an opportunity to recoup his losses and contemplates stealing the diamonds. Meanwhile, Michael comes face-to-face with an old adversary, Ramon, who hits Michael with some hard truths.

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.

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 Malcom and takes him to Ryan for protection. Meanwhile, Percy turns on Alex.

Percy makes a move to take over the CIA, Alex goes rogue, and Michael gets trapped inside Division making him unable to help Nikita, who may have to pay with her life for helping Alex.

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.

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.

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.

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.

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.

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.

Michael gives up his role as a field agent and resumes his role inside Division running Operations. After learning key information from Birkhoff, Nikita preps a secret mission that takes her into dangerous territory. When Michael and Alex and Ryan find out, they follow her into Kosovo but the outcome has far-reaching consequences for Division.

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.

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.

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.

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 middle.

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.

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.

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.

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.