Thomas attended a birthday party at the Bosley Medical Center where she worked in San Francisco on September 30, 2000; accounts differ as to whether the party was in her honor or for a co-worker. She was left the party at 9:00 p.m., driving her vehicle, which was either a gray four-door 1989 Mazda 323 or a 1986 Mazda 626. A friend saw her get on the freeway to return to Hayward. She was photographed at an automated teller machine (ATM) later that evening, and shortly after that her apartment manager saw her doing laundry at the Riverside Terrace apartment complex in the 1700 block of B Street in Hayward. She drove away from there at 10:30 p.m., with her boyfriend following her in his car. Thomas has never been heard from again. Her boyfriend reported her as a missing person to authorities when she failed to pick up her young child.

Thomas's vehicle was discovered abandoned on October 5, 2000, five days after her disappearance. Her car was unlocked and parked at B Street and Watkins Street in downtown Hayward, a block from the Bay Area Rapid Transportation (BART) station. There was no sign of Thomas at the scene, but her purse and her driver's license were found on the front seat of her vehicle. Her car keys were never located.

An extensive search of the Hayward Area produced few clues as to Thomas's whereabouts. Her boyfriend was questioned by authorities afterwards and was reported to have cooperated with investigators. He has neither been named nor eliminated as a suspect. No arrests have been made in connection with Thomas's case. Foul play is suspected in her disappearance.