Plot summary
After Michael learns that Percy has ordered Division to kill anyone who could decrypt the black boxes, he sends Nikita in to save the last person on the list: a CIA cryptographer named Malcolm Mitchell. Nikita saves Malcolm from Division assassins and takes him to Ryan for protection. Meanwhile, Percy learns Alex is the mole. Later, Percy shows Alex visual and audio evidence that it was Nikita who killed her father. Nikita asks Michael to check on her; when Percy orders him to kill Alex, Michael turns the gun on him, but is stunned when he tries to fire it.
Percy reveals that he is several steps ahead of them, even allowing Nikita to have the small victories to ambush her in the end. Percy allows the release of Alex to apprehend Nikita, but under monitoring in case she deviates from the plan. When Alex meets Nikita, Alex asks her if she killed her dad. When Nikita does not answer the question, Alex shoots her.
Credits
Adapted from Wikipedia contributors, Nikita season 1. HTML formatting and reference markers removed.