Nikita seeks revenge on those who betrayed her, making it clear to her former boss and former friends that she will stop at nothing to expose and destroy them. Meanwhile, the organization continues to recruit and train other young men, turning them into cold, effective killers.
As Nikita attempts to thwart Percy and Michael's plan, Alex is prepared early for a special mission, and a flashback reveals a pivotal moment in Nikita's life.
Nikita rescues journalist Jill, who is trying to uncover a conspiracy. Michael and Percy suspect Birkhoff is Nikita's special agent and send Amanda to interrogate him. Michael enlists Alex, Jaden, and Thom to help them locate their latest target.
Nikita delves into her past when she impersonated a powerful government official's nanny and decides to right his wrong. Michael rescues her during that mission and begins to question Percy's motives, while Alex suffers a panic attack during basic training.
The squad's secrets are at risk of being exposed when Agent Owen goes on the run after a failed bank robbery. Percy and Owen then plan to kill each other, but Nikita saves the day. Alex sneaks into Percy's office and is arrested.
During a training exercise conducted by the squad, terrorists attack a bus full of recruits, kidnapping Alex and Thom and torturing them. Alex is freed and turns to Nikita for help. Nikita gains Owen's trust and reveals shocking news to him.
Alex warns Nikita that one of the recruits has been prepped for a suicide mission. Acting quickly, Nikita intercepts the recruit just as Michael arrives on the scene, triggering a fierce gunfight between both sides. Amid the chaos, another recruit launches an attack on several guards, plunging the compound into turmoil.
Thom is asked to eliminate Anna, a woman who was having an affair with the US senator they are blackmailing to fund the organization. Nikita, with Alex's help, tries to contact Anna's parents, but the conversation does not go as she expected.
Michael and Nikita team up to kill a terrorist who killed Michael's family years ago. However, Percy learns this information and sends agents to kill Nikita, jeopardizing the mission. Alex is caught searching the Division's medical files.
Owen leaks classified information regarding the US government's responsibility for an assassination in Chile, implicating a CIA agent. Nikita and Owen head to Chile to rescue him, but are captured.
The Division sends Alex to kill a criminal gang leader, and Nikita insists on helping her. Meanwhile, Birkhoff tells Percy and Michael about a secret program the Division's spy is using to communicate with Nikita in the outside world.
After Alex becomes an agent, she gets a new apartment and is offered undercover work. She meets her neighbor, Nathan, and Nikita warns her against getting too involved with people. Nikita discovers that the Division has implanted a deadly chip in Alex's head.
Alex is assigned to a group mission to kill the prince of Georgia. She tells Nikita about it, and they devise a plan to thwart the assassination. However, Nikita trusts the wrong person, and their plans are foiled. Percy sends Michael to kill Nikita.
Ryan discovers a dangerous weapon being delivered to the United States and asks Nikita to help him stop it. Nikita discovers she knows the man bringing the weapon into the country, and Michael interferes in Alex's new life with Nathan.
While out on a mission, Alex meets her former friend Irina and tries to help her free herself from her kidnapper, but Irina betrays Alex and hands her over to a Russian gangster trying to settle old issues, so Nikita sets out to rescue her.
Amanda drugs Alex after her last mission to speed up her recovery, then takes advantage of Alex's drugged state to question her about the secrets she believes she's hiding. Meanwhile, Nikita's efforts to rescue Alex are disrupted, and she faces a surprising opponent.
Michael confronts Nikita at her hideout and reveals that he knows Alex is the spy. He tells Nikita that she has 24 hours to find Qasim, the man who killed Michael's family, or he will expose Alex to Percy.
Owen returns with information about one of Percy's black boxes, so Nikita goes with him to London to retrieve it, but she notices Owen's strange behavior, and he turns on her. However, Percy discovers Nikita's presence in London, so he sends Michael to kill her.
Nikita plans to protect Alex and hide her, but Alex and Jaden are assigned an outside mission to prevent a foreign president's son from selling a newly developed neurotoxin. Things go wrong, and Alex must choose between saving the mission or saving herself.
Percy sends Michael to check one of the black boxes and the guard attached to it, but Nikita arrives before him and discovers that the guard is an ordinary woman named Dana. On the other hand, Alex and Jaden fight, with Nathan caught in the middle.
Michael discovers that Percy ordered Davison to kill anyone who can decode the black boxes, so he sends Nikita to rescue and protect a CIA cryptographer named Malcolm, while Percy turns on Alex.
Percy makes a move to take control of the CIA, Alex becomes a rebel, and Michael is trapped within the department, leaving him unable to help Nikita, who may have to pay with her life to help Alex.