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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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 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.

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.

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.

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.

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.

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.

When Nikita worked for Division, she targeted a man named Nicholas Brant 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.

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.

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.