"El Cortez" is the story of an autistic man who attempts to start a new life after his incarceration. After five years in a prison for the criminally insane, Manny (Lou Diamond Phillips) returns to Reno. He moves into a motel and takes a job as a clerk at the Hotel El Cortez. He is befriended by Popcorn (Bruce Weitz), a crippled prospector who seeks his help to persuade Russo (Peter Onorati), a wealthy gambler, to invest in Popcorn's gold mine. But Manny cannot escape his past. He is hounded by Arnie (James McDaniel), the vengeful cop who arrested him. Arnie leans on Manny to keep tabs on Jack (Glenn Plummer), a dealer who is staying at the hotel. In the meantime Jack's girlfriend, Theda (Tracy Middendorf), learns about the gold mine and starts putting the moves on Manny. Soon Manny is caught in a labyrinth that leads to a murderous triple cross.