While living in a crime-ridden neighborhood, young, beautiful Nikita Samuelle is wrongly accused of murdering a police officer who had been harassing and blackmailing her. Expecting life imprisonment, Nikita instead finds herself forced to work for a ruthless, top-secret government organization, Section One, which stages a fake suicide to cover her disappearance. Under the tutelage of a mysterious agent named Michael, Nikita must learn to suppress her compassion and develop the lethal skills that the government thinks she already possesses.

Waiting at a café for an informant who will advise her who the next Section One target will be, Nikita is recognized by her longtime friend Julie, who knew Nikita before she went undercover with Section One. When the informant sees that Nikita is not alone, he refuses to give Nikita the information. Michael tells Nikita that, because Julie recognized her, Julie must be killed--either by Nikita or someone else. However, what Nikita does not know is that Julie is actually Section One's next target.

Section One infiltrates a terrorist organization that uses a radar-cloaking device to cause midair collisions between airliners. This is the same organization that supposedly killed Michael's wife, Simone. Nikita poses as a terrorist to locate the deadly mechanism and learns that Simone has not been killed but has been held as a prisoner and tortured for two years.

During a routine assignment, Nikita saves an attractive man, Alec Chandler, from being hit by a car. When he asks her on a date, she declines but gives him information about where she works so he can send her a present. Nikita learns that the near-accident was staged by Section One so that Nikita could gain information about Alec's criminal activities. Michael informs Nikita that Alec is a slave trader who sells children around the world--not a money launderer as she was first told. Nikita exposes Alec's operation, saving a group of helpless children from a horrible fate. But Michael, who is becoming attracted to Nikita, will never know if Nikita ever made love to Alec.

Criminals John Wicke and his wife, Helen, obtain a nuclear trigger, intending to sell it to the highest bidder. During a failed purchase attempt, four Section One operatives die in an explosion. Helen continues her search for a child she put up for adoption while still a teenager--and a prison inmate. In a scheme devised by Section One, Nikita pretends to be Helen's long-lost daughter. Nikita kills John while searching for the trigger. Posing as police officers, Michael and a group of operatives arrest Nikita and her "mother" and beat Nikita to force Helen to reveal information about the trigger in order to save her supposed daughter.

Section One intercepts a husband-and-wife bodyguard team hired to work for terrorist Perry Bauer. To gain information on Bauer's next strike, Section One assigns Michael and Nikita to impersonate the captured couple and infiltrate Bauer's operation. After determining that Bauer plans to release poisonous gas into a crowded subway station, Michael and Nikita overcome Bauer's thugs and trap him in the station. Fearing for his life, Bauer tells Michael and Nikita how to prevent the crisis. Later, Michael and Nikita are disgusted to learn that their government will let Bauer go free.