In the season finale, Amanda puts her final plan in motion and forces Nikita into a life-threatening situation where she has to choose between saving Michael ... or saving herself.
Michael questions Nikita's commitment to a life beyond Division's web - and he's not the only one with doubts. Alex considers an intriguing offer from a Nobel Prize winner.
Nikita, Michael, Alex and arms dealer/reformed rogue agent Cyrus (ISIAIH MUSTAFA) stage a daring operation at the tightly secured G20 economic summit.
Dirtied with Division blood and destruction, an emotional Alex reverts to old ways and violently strikes out. Birkhoff struggles with his own personal losses.
Strapped down and drugged, Nikita is subjected to Amanda's horrific mental conditioning process, sending her on 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.
Alex confesses to Birkhoff her desire to leave Division. Amanda begins providing Owen with something he was never able to find - memories of his real past. Despite Nikita's attempts to help, Owen begins to confront the events of his past.
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.
When Nikita decides Division should take on a government mission to eliminate the President of Chad (guest star JONATHAN ADAMS – Revenge) while he's in Paris, Alex takes a stand and refuses to participate. Upset that Nikita is keeping secrets from everyone, much like Percy did, Alex recruits Birkoff to dig up secrets on Danforth (recurring guest star RICHARD T. JONES – Hawaii Five-O) to use as leverage in case things get messy with the government. Alex and Birkhoff are shocked when they come across a secret so big it could blow up Division - literally.
Amanda holds Alex hostage and tells Nikita she will release Alex in exchange for Ari (recurring guest star PETER OUTERBRIDGE). Michael assigns Nikita and Sean to handle the exchange of prisoners, but Ryan adds Owen to the team at the last minute, which makes Michael suspicious. While in captivity, Alex befriends a fellow prisoner named Larissa (guest star OLGA FONDA – How I Met Your Mother) and vows to break them both out of the jail, which ultimately conflicts with Nikita's plan, forcing Alex to choose between Nikita and her promise to Larissa.
In order to gain control of the black box, Amanda makes plans to kidnap Ari's (recurring guest star PETER OUTERBRIDGE) son, Stefan(guest star DYLAN MINNETTE – Saving Grace, Awake) to use him as leverage. Still in Division's protective custody, Ari begs Nikita for help. However, Stefan's bodyguard, Krieg (guest star ANDREW DIVOFF – Lost) 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 backup instead of him.
After Birkhoff gets a tip from Shadow bot that Ari (recurring guest star PETER OUTERBRIDGE) is in New York, Nikita and Owen swoop into pick him up before the FBI does. However, Ari reveals he planned everything for a chance to talk to Nikita. He tells her that Amanda has gone too far and is working with a terrorist who plans an attack on American soil. Ari wants 50 million dollars for the information that could lead to the terrorist's (guest star PITER MAREK – Castle) capture. Nikita and Michael are stunned when Ryan considers paying the bribe. Meanwhile, Sean is jealous of Alex and Owen's relationship.
A CIA agent named Naomi (guest star AMANDA SCHULL – Pretty Little Liars, One Tree Hill, Center Stage) comes across a file detailing Madeline Pierce's involvement with Division and turns it over to the Director of the CIA, Morgan Kendrick (guest star BRIAN HOWE). When Kendrick is killed shortly thereafter, Amanda frames Sean for the assassination and the CIA takes him into custody. Nikita promises Alex they will free Sean and comes up with a plan that could either save him or cost him his life.
Michael gives up his role as a field agent and resumes his role inside Division running Operations. After learning key information from Birkhoff, Nikita preps a secret mission that takes her into dangerous territory. When Michael, Alex and Ryan find out, they follow her into Kosovo but the outcome has far-reaching consequences for Division.
A rogue agent named Ray (guest star MATT BUSHELL – True Blood) kidnaps his girlfriend, Kate (guest star ANNA HOPKINS – Barney's Version), so Ryan dispatches the team to rescue her. Nikita is confused when Michael sends Owen into the field with her instead of going himself. Meanwhile, Sean makes a decision about Alex.
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.
Birkhoff tells Nikita that Sonya (recurring guest star LYNDIE GREENWOOD) is Amanda's mole and not only has Amanda reactivated Sonya's kill chip but she also placed a second mole in Division to keep an eye on her. Nikita, Michael and Ryan devise a plan to use Sonya to ferret out Amanda's hiding place and Birkhoff sets a trap for the second mole. Meanwhile, Michael confronts Alex about her drug use and she begs him not to tell Nikita.