Tensions continue to escalate between the United States and Pakistan after Amanda plants evidence that Pakistan hired Nikita to kill the President. Ryan becomes suspicious of Birkhoff's increasingly odd behavior and tells Nikita and Michael that he thinks Amanda may have kidnapped Birkhoff and planted a double on the plane. Meanwhile, the CIA captures Alex and questions her about her involvement with Nikita.

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.

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.

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.