The season finale begins where we're glad it didn't end, with a cleaner getting ready to dispose of Nikita's dead body. But it turns out Alex shot her cohort with a tranquilizer, not real buckshot. Luckily some face-melting acid is at the ready when she revives. The cleaner gets it and Nikita gets out.
She immediately runs for CIA HQ, knowing that Alex set nerve gas on the black box that the CIA was currently trying to decrypt. This is all part of Percy's plan to take out the head of the CIA with the nerve gas and then take over the agency. And of course, Percy knows saving him will be Nikita's next move, so he orders a sleeper agent on her tail immediately. After killing him, Nikita makes it into HQ just in time to save Fletcher and team. Before they can make a clean escape, an agent handcuffs Nikita. Luckily Fletcher still has the wherewithal to save her and the two make a break for it. But Nikita still has to make her getaway without being stalked by Division henchmen.
Meanwhile, Berkoff still has Michael in cuffs. Feeling guilty, he cuts him loose using a remote computer. Once free, Michael goes directly to Percy's safe and grabs another Operation Sparrow black box, which he then brings to Berkoff for decrypting. Eventually the two hook up to help Nikita to safety by guiding her through a computer device, but they lose their connection with her. Nikita quickly escapes through an air vent and then hops onto a garbage truck leaving HQ.
Poor Alex, hell bent on avenging her father, finds herself back with a Division team and in the capable hands of Amanda and her torture chair. After a short interrogation, Amanda suddenly zaps Alex unconscious only to revive her with an adrenaline shot. Apparently, this deactivates the kill chip installed in Alex to make her go after Nikita. In a truly shocking move, Amanda let Alex go, telling her to stay away from Nikita.
Alex goes straight to Nikita's loft, of course. Nikita isn't sure if she can trust Alex anymore. Before they can fully clear the air, Division spooks storm Nikita's loft, which she was in the middle of rigging for explosion anyway. The two make their getaway on the roof. Nikita zip lines over to the next building, but Alex stays behind and gets herself back in Division custody.
Nikita meets up with Michael, who now has a freshly decrypted black box in his possession. Michael and Nikita drive off, discussing their next move and future together.
Unfortunately Alex, she's facing the same prospects she had at the beginning of the episode. Will she succumb to a new Division group, even with Amanda still within its ranks?
The senator from Oversight who Percy meets with in the restaurant and who appears again in front of Alex at the end of the episode is played by Alberta Watson, who played Madeline, the role equivalent to Amanda, in the original La Femme Nikita series.