U.S. Marshal Jack Carter is transporting a high-priority fugitive — his runaway teenage daughter ZoŽ — 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 Defence, 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.
That earns Jack some respect but no more details about what's really going on in this bizarre town. Only after another vortex nearly kills Sheriff Cobb does Blake finally admit that she could use Jack's help. She hands him a book-length nondisclosure agreement and orders him to sign. Then she reveals the town's secret: Eureka was established after World War II as a covert haven for the nation's greatest scientists. Its centrepiece is the Advanced Research Facility, a vast underground structure crammed with exotic projects and dedicated researchers. The only area that Blake won't show Jack is Section 5, where an obsessively clandestine team works on military projects.
Despite all this brainpower, however, no one will admit to knowing what's causing the devastating vortices, and Jack can't prove his suspicion that Section 5 is involved. That night, yet another vortex rips through the town's diner, killing a man. The crisis is growing steadily worse.
Jack, Blake and Deputy Jo Lupo trace the origin of the disturbances to the Perkins residence. There, Brian's panicky mother explains that her husband has locked himself in the basement, desperate to fix major problems with a top-secret experiment he's been conducting.
Jack and Lupo force their way into Dr. Perkins's lab, where they discover a ringed device spitting out arcs of blue energy. It's a prototype tachyon accelerator, built to generate faster-than-light particles. Now out of control, it has apparently killed its creator and yielded a catastrophic side effect: all the laws of physics have begun to corrode. Soon, the town will be one vast vortex, and eventually the whole planet will be ripped apart.
Although Jack is a stranger to quantum physics — and really just wants to protect his daughter — only he holds the key to solving this cosmic disaster. And, assuming he succeeds, he'll have a job waiting for him: as the new sheriff of the strangest town in the country.