Alex's mission to take down Gogol comes to a head as she infiltrates her childhood home and faces ghosts from her past. On a completely separate mission, Nikita also ends up at the mansion to steal Semak's black box. Nikita and Alex run into each other and decide to join forces, but they run into a major roadblock. Meanwhile, Michael and Owen work together to figure out Percy's secret plan with the Guardians.
Amanda and Percy reach an agreement in which she would release him in exchange for the Clean Sweep trigger. While Nikita, Michael and Sean head to the Gates House to save the members of Oversight that are hostages of Percy's Guardians Alex heads to Division to stop Clean Sweep from being activated. But not everything goes as expected.
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.
Nikita and Michael try to help Carla remember her past, which holds the key to taking down Division. Carla recounts the night Nikita was arrested and Nikita is stunned at what she learns. Meanwhile, Alex shows up at a Zetrov press conference where Semak is speaking and announces that she's Alexandra Udinov. Alex demands a trade - her mother for the empire.
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.
Michael is furious when he discovers a secret that Cassandra kept from him, so he and Nikita fly to Moscow to confront her. Meanwhile, Alex makes a last ditch effort to find her mother by sending out a coded message through a televised interview.
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 breaks a man out of prison because he wants something from him. The man won't give it to him unless Percy gives him the one who placed him in prison, Nikita. So the man, on advice from Percy, tries to lure her out by killing Senator Pierce. So they all stake out the funeral but he manages to get Nikita. So he subjects her to torture but she doesn't break. When Percy asks for what he wants, the man refuses to give it cause she's not breaking. Percy then makes Michael turn himself to the man, he then tortures Michael in front of her.
Division, now under the leadership of Ryan Fletcher, is tasked by the government to track down 30 rogue agents, nicknamed the "Dirty Thirty", who refused the recall order. One such agent is Martin, who is selling his services to Chinese Intelligence to eliminate undercover CIA operatives. As Michael and Nikita attempt to bring him in, Nikita is faced with saving one of her own or risk an international incident when Michael - who in the middle of trying to propose to Nikita, is arrested for murder.
Rogue agent Wade, who used to train Division recruits before beating one to death for failing to kill his target, has been revealed to have kidnapped a young girl and trained her as a child-soldier. While he prepares her for battle, Nikita and Alex try to help the girl and reunite her with her family before she kills the Pakistani ambassador.
Mia, an undercover Division agent investigating the domestic terrorist group, Third Wave, is arrested during an FBI raid. When Nikita and Alex spring her, she turns on them, revealing to having lost faith in Division and having joined Third Wave's cause. But as Division discovers, Third Wave's leader is in league with the head of a security firm, using the group to attack a U.S. Senator to make more money.
A former agent now working for Amanda springs Owen from a Russian prison, who escapes and contacts Nikita for help. After a biohazard is released inside Division, Birkhoff and Sonya suspect a mole working for Amanda on the inside. Sean fears for Alex's safety.
Undercover for six years, rogue Division agent Markov has been elected President of Uzbekistan and plans to kill the President of the United States. Ryan informs the team that the President has threatened to dismantle Division if the public finds out about them and their rogue agents, and must figure out how to save the President's life without alerting her of the danger. Meanwhile, Alex uncovers a murder plot against Owen.
Nikita and Michael capture Cyrus, an arms dealer, who is purchasing a weapon-jamming device for Ari. Nikita convinces Ryan to let them use Cyrus as bait to capture Amanda but Cyrus manages to escape the trap. However, when Amanda double crosses Cyrus, his only hope for survival is Nikita. Meanwhile, Birkhoff is hot on the trail of Amanda's mole and Alex starts to unravel.