U.S. Marshal Jack Carter is transporting a high-priority fugitive — his runaway teenage daughter Zoe — back to Los Angeles. Unfortunately, he's also lost on a lonely back road. When he accidentally wrecks the car, father and daughter find themselves stranded in an odd little town called Eureka, where the children are geniuses and the car mechanics are former NASA engineers.

As he waits for his car to be fixed, Jack gets caught up in an urgent search for a missing local child, Brian Perkins. The boy has just disappeared in a freak accident — a very freak accident: he's apparently been swallowed by a mysterious vortex that burned off the back half of his parents' R.V. Although Eureka's world-weary sheriff, Bill Cobb; his deputy, Jo Lupo; and even an agent from the Department of Defense, Allison Blake, warn Jack to back off, he refuses to quit. Soon, by spotting clues that everyone else has missed, he discovers that the supposedly lost kid is still hiding in the R.V.