When she was a deeply troubled teenager, Nikita was rescued from death row by a secret U.S. agency known only as Division, who trained her as a spy and assassin. Nikita was eventually betrayed by the only people she thought she could trust. Now, after three years in hiding, Nikita is seeking retribution and making it clear to her former boss, Percy and her former friends Michael and Birkhoff that she will stop at nothing to expose and destroy their covert operation. Division continues to recruit and train other young people, among them Jaden and Thom, erasing all evidence of their former lives and turning them into cold and efficient killers. One of these new recruits, Alex is a beautiful girl with a violent past and a story not so different from Nikita's. The recruits all spend part of their training with Amanda, a master manipulator who can turn any ugly duckling into a swan and any bleeding heart into a killer.

Percy and Michael take their latest assignment, a Slavic leader wanted for war crimes, into protective custody. Nikita learns of their hideout and attempts to thwart their plan, but a mysterious group of mercenaries in search of nuclear material beats her to the task. Alex is activated earlier than expected for a special assignment that throws her into the crossfire of bullets. A flashback reveals a pivotal moment in Nikita's life.

Nikita rescues Jill, a journalist who is trying to expose a conspiracy involving Division and a major plane crash. Michael and Percy suspect Birkhoff of being Nikita’s inside mole and send Amanda in to interrogate him. Meanwhile, Michael enlists the help of the recruits, Alex, Jaden and Thom, to help them locate their latest target.

Nikita delves into her past when she posed as a nanny for an influential government official and decides to right the wrong of his death. During the mission, Michael comes to Nikita’s rescue and begins to doubt Percy’s motives. Back at Division, while undergoing basic training, Alex suffers from a panic attack which prompts Amanda to break her of claustrophobia.

Divison’s secrets are at risk of being revealed to the world when Owen, a Division operative, escapes from a bank robbery and becomes a fugitive. Percy decides to search for Owen himself, which makes Michael suspicious of his motives. Meanwhile, Alex sneaks into Percy’s office to warn Nikita, but she is busted by Thom. In the end, Nikita and Owen go head-to-head until Percy joins them for a tense standoff.

A bus filled with Division recruits is attacked by terrorists who kidnap Alex and Thom, both of whom are unaware that this is a test by Division. Percy, Michael and Amanda watch as Alex is tortured. Alex breaks free and contacts Nikita for help. Meanwhile, Nikita has earned Owen's trust and he reveals some devastating news to Nikita about her fiancé.

Alex informs Nikita that one of the recruits has been activated to carry out a suicide mission.

Division sends Thom to eliminate Anna, a woman who was having a secret affair with a U.S. Senator. Division agrees to cover up any trace of the affair as long as the Senator agrees to help pass a bill that will continue to fund the agency. Nikita, with Alex's help, attempts to reach out to Anna's parents, but the conversation doesn't go as she expected.

Nikita and Michael temporarily team-up to kill a terrorist who murdered Michael’s family many years ago. When Percy learns this information, he sends Division agents to kill Nikita, who ultimately compromises the mission, leading to Michael’s capture by the terrorist group. Alex is caught going through medical files inside Division so she creates a lie that involves Jaden and almost blows her cover.

Owen leaks secret information from Division’s black boxes to the media, revealing that the U.S. Government was responsible for an assassination in Chile. As a result, Percy frames a C.I.A. agent, Ryan for the crime. Nikita and Owen go to Chile to rescue Ryan from mercenaries and in doing so end up getting captured. Nikita reveals the secrets of Division to Ryan in an effort to save all of their lives. Back inside Division, Alex spies on Percy and Birkhoff and witnesses a side to Percy she has never seen before.

Alex informs Nikita that Division is sending her on her first mission to kill the leader of a crime syndicate. Alex is uneasy about taking someone's life but is reassured by Nikita who insists on helping her with the kill order. Birkhoff informs Percy and Michael when he discovers the shell program that a Division mole has been using to connect to Nikita in the outside world. When the mission doesn't go as planned, Nikita makes a quick decision in an effort to clear Alex's name. Inside Division, Jayden attempts to reveal Alex as the mole but Thom steps in and a shocking accident clears her name.

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 information about a dangerous new weapon coming into the U.S. and asks Nikita to help him prevent its delivery. Nikita learns that the man bringing the weapon into the country is Voss, a man Division forced her to have a relationship with while working undercover. She reluctantly resumes her alter ego to prevent the weapon from being delivered. Meanwhile, Michael interferes with Alex's relationship 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 middle.

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.

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.

Ray (Matt Bushell), a rogue agent, kidnaps his girlfriend Kate (Anna Hopkins), 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 (Dylan Minnette) to use him as leverage. Still in Division’s protective custody, Ari begs Nikita for help. However, Stefan’s bodyguard Krieg (Andrew Divoff) 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 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.