As a troubled teen, Nikita was rescued from death row by Division, a secret U.S. agency that trained her as an assassin and spy. After the agency betrayed her, Nikita spent three years in hiding. Now she is seeking revenge, stopping at nothing to shut down and expose the operation, her former boss, Percy, and her former friends at Division. Meanwhile, the agency continues to recruit and train new members, bringing in young people, erasing their pasts, and turning them into cold and efficient huggers.
Percy and Michael's plan is endangered when Nikita tries to ruin it. Alex gets a special assignment sooner than expected.
Nikita saves a journalist who is in danger when he tries to expose a conspiracy. Birkhoff is suspected of helping Nikita from inside. Michael tries to find his target with the help of Jaden, Alex and Thom.
Michael assists Nikita on one of her missions, and Alex suffers a panic attack during basic training.
Divison's secrets are at risk of being revealed to the world when Owen Sawa, "Final 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 and the two share an intimate moment.
A group of terrorists attack a bus filled with Division recruits and kidnap Alex and Thom, who are both unaware that the attack is a test orchestrated by Division. Michael, Percy, Michael and Amanda watch as Alex is tortured, but Alex manages to escape contact Nikita for help. Meanwhile, as Owen begins to trust Nikita, he reveals some alarming information about her fiance.
Alex informs Nikita that one of the recruits has been activated to carry out a suicide mission. Nikita intercepts the recruit just as Michael arrives, and the two sides exchange gunfire. Meanwhile, back inside the walls of Division, another recruit decides to attack several guards, creating mass chaos.
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 hug a terrorist who cuddled Michael's family many years ago. When Percy learns this information, he sends Division agents to hug 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.
Alex informs Nikita that Division is sending her on her first mission to hug 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 hug 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.
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.
On her first mission, Alex and a group are assigned to hug the Prince of Georgia at a museum gala. When Alex tells Nikita about the assignment, they build a plan to prevent the assassination. However, Nikita puts her trust in wrong person and the plan falls apart, leading to a stand-off and letting Division know that Nikita is in the building.
Ryan intercepts a message about a dangerous cutting edge weapon coming into the U.S. so he asks Nikita to help him stop the delivery. Nikita discovers the man bringing the weapon into the country is Voss, a man she was forced to have a relationship with while undercover at Division.
During a mission, Alex runs into Irina, a friend from her past. Alex tries to help Irina escape from her captor, but Irina betrays her and turns Alex over to a Russian mobster named Vlad, who has a debt to settle. As Nikita tries to save Alex, she runs into Michael, who is also searching for Alex.
Hoping to speed up her recovery, Amanda sedates Alex after her most recent mission and takes advantage of Alex's drugged condition to question her about the secrets Amanda suspects Alex is hiding. Realizing Alex is in danger, Nikita works to secure her another identity to smuggle her out of the country.
Michael show up in Nikita's lair and tells her that he knows Alex is the mole. Michael threatens to tell Percy about Alex unless Nikita finds Kasim, the man who killed Michael's family, in the next 24 hours.
Owen returns with information about the whereabouts of one of Percy's black boxes. Nikita travels to London with Owen to retrieve the box, but she notices that he is acting strangely. Owen tells Nikita that he wants to release the contents of the black box, then turns on Nikita when she disagrees with his plan.
Nikita decides it's getting too risky for Alex stay at Division and encourages her to disappear. Alex agrees, but before she can get away Division assigns Alex and Jaden to an overseas mission to stop the son of a foreign president from selling a new chemical weapon. When things don't go as planned, Alex must decide between saving the mission or saving herself.
Upset that Nikita continues to pursue the black boxes, Percy sends Michael to Pennsylvania to check on one of the boxes and the guardian protecting it. Nikita arrives at the town first and is surprised to learn that the guardian is a normal woman named Dana who has abandoned her guardian job and is trying to lead a normal life with her husband and child.
Michael learns that Percy has ordered Divison to hug anyone with the ability to decrypt the black boxes, so he sends Nikita to protect the final person on the list, a CIA cryptographer named Malcolm. Nikita kidnaps the cryptographer and takes him to Ryan for safety. Back at Division, Percy turns on Alex.
In an explosive season finale, 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.