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... 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. Nikita and Owen go head-to-head until Percy joins them for a tense standoff. Alex sneaks into Percy’s office to warn Nikita, but she is busted by Thom.
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.
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 Fletcher 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 missile 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.
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.
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.
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 Sonya 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 kill 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 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.
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.
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.
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.
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.
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.