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 gain control of the black box, Amanda makes plans to kidnap Ari's son Stefan (Dylan Minnette) to use him as leverage. Still in Division’s protective custody, Ari begs Nikita for help. However, Stefan’s bodyguard Krieg (Andrew Divoff) manages to capture both Nikita and Amanda and the two must work together to escape. Owen is furious with Michael after Michael assigns Alex to be Nikita’s back-up instead of him.

Strapped down and drugged, Nikita is subjected to Amanda's horrific mental conditioning process, sending her down a terrible trip through memory lane. In the process, Nikita discovers Amanda's deepest, most guarded secret ever. Now revealed as leader of the uprising, Alex struggles to save everyone as events violently escalate. With Michael locked away by Division conspirators, Birkhoff and Sean must step up to save the women they love. Meanwhile, Owen's newfound memories drive him to disturbing actions during Division's lockdown.

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.