Section One is hot on the trail of Tyler, one of the world's most dangerous terrorists. After Tyler kidnaps a young inventor who has created a new, completely un-detectable plastic explosive, Nikita is sent to try and rescue the inventor and keep his knowledge out of Tyler's hands. When the mission is unsuccessful, Nikita is given orders to cancel the inventor, but she refuses. Operations decides that Nikita has crossed the line, and he purposely sends her on a suicide mission to destroy a terrorist hideout. Michael intervenes and gives Nikita the means to escape, but her freedom will change both of their lives forever.

With Adrian's help, Nikita manages to breach the most sensitive area of Section and secure a file, code named Gemstone, which contains evidence which will bring down Operations and destroy Section One. Meanwhile, Operations forces Michael to identify the Section operative most likely to work with Adrian to undermine Section, Nikita. Michael confronts Nikita in order to try to find a way to protect her, but she denies any association with Adrian. Now Michael is forced to kidnap both Nikita and Adrian and bring them back to Section, knowing that Nikita and Adrian will be cancelled and that the incriminating Gemstone file will be permanently erased.

An important Center satellite named Comstat Alpha crashes near a small town in Kentucky by the name of Dingman's Hollow. Michael and Nikita are then sent on a mission to retrieve it; the first mission with Birkoff's replacement, Corman. The data it carries, before it falls into the wrong hands. When Michael and Nikita get to Dingman's Hollow, they discover that the satellite is missing from its crash location. Soon enough, Nikita discovers that strange things are afoot in the town of Dingman's Hollow. It turns out that the entire town is a ""Sleeper Base"" for the Black Storm terrorist group, making Michael and Nikita's mission that much more difficult. Meanwhile, Naomi, the girlfriend of Birkoff's brother, Jason Crawford, is taking him to Aruba. Can Section One be far behind?

Michael and Nikita have been traveling from place to place, keeping one step ahead of Section One's attempts to find them. When George is eliminated from the picture after leaking intel to Red Cell in order to discredit Section One, the newly-empowered Operations and Madeline finally track down Michael and Nikita. They bring them back to Section. Just as Michael and Nikita are about to be cancelled, all of Section's systems suddenly stop. Mr. Jones, the mysterious head of Center, is on his way to Section One in order to conduct an evaluation, and has put Section in stasis. When Jones arrives, he is really Nick Shtoppel Nikita's neighbor and Section informant. He reveals that Nikita has been secretly working for Center for the last three years. Nikita assists Jones with his evaluation, and things change radically. Operations is forced to remain at Section One for the next seven years. Madeline takes her own life rather than be cancelled. Walter is transferred to the Farm, where he will