The film opens in 1997 with a scene of an unknown assailant breaking into the home of two sisters. After one goes to sleep, the attacker subdues one of them using halothane and murders her after raping her and torturing her by hanging her upside down with latches and rope. The assailant then rapes and tortures the other sister when she wakes up but she is not killed. After police questioning, the attacker, Jon Forster (Neal McDonough), is convicted by a jury after Gramm testifies against him in court. As Gramm leaves, Forster taunts him, saying "Tick tock Doc."

Nine years later, on the day Forster is to be executed at midnight, several similar torture murders with very similar modi operandi occur. Gramm is questioned but released. On the way to his class, he receives a threatening phone call telling him that he has 88 minutes to live. He reports the threat to Shelly (Amy Brenneman), his secretary, and brushes off the threat. He receives another call while teaching, and he becomes suspicious of the students. A dean, Carol (Deborah Kara Unger), enters the classroom and warns of a bomb threat, telling everyone to leave. Gramm finds written threats in the classroom. He goes to the parking lot to see that his car has been vandalized with a similar threat.

Later, one of his students, Lauren Douglas (Leelee Sobieski), is attacked by an unknown assailant. Gramm reports this to the police after questioning nearby people. He later discovers through a tape that someone had accessed his secure files. On the tape is a little girl, scared, saying Gramm's name many times and asking for help. The sound of a door breaking down and the girl screaming is heard. The screaming stops seconds later. With the help of his teaching assistant Kim (Alicia Witt), Gramm tries to notify authorities while trying to uncover Forster's past at the same time.