Nikita schafft es Birkhoff, den IT-Experten der Division, zu entführen. Sie droht ihm Folter an, wenn er ihr nicht die Passwörter für das Division-Netzwerk verrät.

Percy und Michael sollen einen Diktator und Kriegsverbrecher in Schutzhaft nehmen, aber Nikita spürt sie auf und versucht ihren Plan zu durchkreuzen. Alex erhält ihren ersten Auftrag.

Alex wird auf ihre erste tödliche Mission geschickt. Birkhoff entdeckt das Programm, mit dem zu Nikita Kontakt aufgenommen wurde. Nikita wird von der Division gefangen genommen.

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 and Michael plot to take down Division and Oversight and are prepared to use the contents of the black box to do so. Amanda is now running Division but Oversight has assigned one of their own, a new agent named Sean, to keep an eye on her. Amanda's first mission is to get back the black box from Nikita, and she enlists Alex's help to do so. Alex refuses until Amanda tells her she will help her find the man who killed Alex's father. Meanwhile, Nikita and Michael find help from an unlikely ally.

Ryan takes charge of Division with Nikita by his side. Their first mission under the new regime is to bring in “The Dirty Thirty,” the rogue agents who failed to respond to the Division recall after Percy was killed. Unfortunately, their first mission doesn’t go as planned and Michael is arrested, forcing Nikita to change gears and hatch an escape plan for him. Alex reprises her alter ego, the spoiled Russian princess Alexandra Udinov, in a very unique way as part of the plan to spring Michael. Meanwhile, Birkhoff struggles to maintain a working relationship with Sonya, despite his growing attraction to her.