Primal Fear follows Martin Vail (Richard Gere), a cocky, high-profile Chicago defense attorney who loves the spotlight. He famously only defends clients he believes are innocent. When a beloved Catholic Archbishop is brutally murdered—stabbed 78 times—the prime suspect is a terrified, stuttering altar boy named Aaron Stampler (Edward Norton in his film debut).

In a courtroom twist, Vail flips the narrative. He argues that Aaron is not legally responsible because his "sane" personality didn't commit the crime. He gets Aaron to "switch" on the stand—transforming from the meek, stuttering boy into the violent, confident Roy, who threatens the prosecutor. The jury, horrified by the Archbishop’s crimes and convinced of Aaron’s insanity, finds him not guilty by reason of insanity. Vail has won the impossible case.

As Vail and his team investigate, they uncover that the Archbishop was not a saint. He ran a corrupt housing project, embezzled funds, and—most critically—forced Aaron and another boy into making pornographic videos. Vail argues that Aaron, already psychologically fragile, snapped when the Archbishop tried to assault him again. But the prosecution has a devastating witness: a psychologist who claims Aaron suffers from Dissociative Identity Disorder (DID), meaning a "bad" personality called "Roy" could have committed the murder, making Aaron a danger to society.

Vail takes the case pro bono, not out of altruism, but because the media circus guarantees publicity. He is opposed by his former lover, prosecutor Janet Venable (Laura Linney), who sees the case as her path to a judgeship.