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.
In order to stop Amanda from killing Sonya, Nikita, Michael and Ryan use Sonya to find Amanda's hiding place and Birkhoff sets a trap for the second mole while he tries to deactivate Sonya's kill chip. Michael confronts Alex about her drug use.
Nikita and Owen face off against a rogue "cleaner" named Liam (guest star PEDRO PASCAL - The Good Wife), while Michael takes a new position at Division. Michael and Nikita's relationship becomes strained as he watches her work with Owen.
Nikita and Michael learn of a new prosthetic hand that could have Michael back to his old self, but it comes at a steep price. Meanwhile, Alex and Sean are tasked with investigating who inside Division is behind a mutiny that ends in bloodshed.