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.

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.

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.

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.

After Michael learns that Percy has ordered Divison to kill anyone who could decrypt the black boxes, he sends Nikita in to save the last person on the list, a CIA cryptographer named Malcolm. Nikita kidnaps Malcom and takes him to Ryan for protection. Meanwhile, Percy turns on Alex.

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.

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 Birkoff gets captured. 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.

Sean attacks Nikita and Michael in an effort to protect his mother. Meanwhile, Percy gets the upper hand on Amanda and threatens to level Division unless she releases him.

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.

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.

Michael confronts Nikita in her lair and reveals that he knows Alex is the mole. He tells Nikita that she has 24 hours to find Kasim, the man who killed Michael’s family, or he will tell Percy about Alex.

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.

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.

Amanda forces Nikita into a life-threatening situation where she has to choose between saving Michael or saving herself. The team races to find a way to stop Amanda, but with a diminished Division, they might finally be out-gunned.

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.

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.

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.

While in prison, Ryan Fletcher 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 Ryan 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.

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. Meanwhile, Amanda realizes that Alex has acquired 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.

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.

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.

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.

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.