While protecting a man due to testify against the Morley cigarette company, Skinner is horrified when the witness dies mysteriously. What the agents soon discover is that a new brand of cigarette has a dangerous secret.

A prominent lawyer wakes to find himself in jail and about to be prosecuted for the murder of his wife. He has no memory of this event however, and when the days begin to regress backward towards the murder, he realizes that he has been given a second chance.

Mulder and Doggett are reluctantly thrown together to investigate several deaths aboard an oil rig, and Mulder becomes convinced that the rig is really carrying the black oil alien.

During a stakeout of murderer Irwin Lukesh, Doggett sees Reyes attacked by Lukesh, but then we see Reyes and Doggett in her apartment, apparently both fine. Elsewhere at the same time, Doggett is shot and Lukesh identifies Reyes as the shooter. While Reyes is asked for her badge and gun by A.D. Follmer, and Doggett lies in hospital near death, the conflicting circumstances of the stakeout and Doggett's shooting do not add up and it becomes clear that Lukesh possesses the power to switch between parallel universes and alter the events in each.

After a car accident, Reyes finds herself in a very gray area, while Doggett desperately denies doctors' diagnoses about his partner, who witnesses a strange disappearance.