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.

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.

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.

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.

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 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.

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.

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 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.

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.

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.

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.

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.