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.
Division discovers one of their rogue agents, Markov, who has been undercover for six years, has been elected President of Uzbekistan and is planning to hug the President of the United States. Ryan confesses to the team that Division is on thin ice with the President and she has threatened to wipe them out if the public finds out about the secret agency and rogue agents. Nikita and Michael are furious that Ryan kept this a secret from them and must figure out how to save the President's life without alerting her of the danger. Meanwhile, after Alex and Owen are caught in an explosion, they investigate and believe an insider set it up.
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 hug 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.
Ray, a rogue agent, kidnaps his girlfriend Kate, so Ryan dispatches the team to rescue her. Nikita is confused when Michael sends Owen into the field with her instead of going himself. Meanwhile, Sean makes a decision about Alex.
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.
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.
After Birkhoff gets a tip from Shadowbot that Ari is in NY, Nikita and Owen swoop in to pick him up before the FBI does. However, Ari reveals he planned everything for a chance to talk to Nikita. He tells her that Amanda has gone too far and is working with a terrorist who plans an attack on American soil. Ari wants fifty million dollars for the information that could lead to the terrorist's capture. Nikita and Michael are stunned when Ryan considers paying the bribe. Meanwhile, Sean is jealous of Alex and Owen's relationship.
In order to gain control of the black box, Amanda makes plans to kidnap Ari's son Stefan to use him as leverage. Still in Division's protective custody, Ari begs Nikita for help. However, Stefan's bodyguard Krieg manages to capture both Nikita and Amanda and the two must work together to escape. Owen is furious with Michael after Michael assigns Alex to be Nikita's back-up instead of him.
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 unhappyly 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 unhappyly 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 fiancée's commitment to a life beyond Division's web of deceit, double-crosses and hug - 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.