The series concludes with Nikita seeking revenge against MDK. She captures Jones and forces him to give her the names of MDK members. Michael tracks her down and tries to get her to surrender before the military opens fire and kills her.
Ryan confesses a secret that threatens to unravel Nikita's world. Meanwhile, Alex gives Sam a suitcase of fake diamonds to deliver to a contact in France when she suspects that he is planning on stealing them.
Jones benches Amanda and takes back control of the operation and offers her and the team complete freedom by wiping away their identities and faking their deaths if they will walk away from the mission. When their plane lands in Pakistan it is overtaken by a local drug czar and his thugs who demand $10 million.
Tension escalates between the U.S. and Pakistan after Amanda plants evidence that Pakistan hired Nikita to kill the president. Meanwhile, Ryan suspects that Amanda kidnapped Birkhoff; and the CIA captures Alex and questions her about Nikita.
Amanda makes doubles of VIPs with the Shop's help; and Nikita discovers that one of the doubles is the FBI director. Meanwhile, Alex holds Sam at gunpoint and demands that he return what he stole from her, but they are forced to work together when a gang attacks them.