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Thora was last seen outside Campbell High School in Campbell, California on November 2, 1945. She had just finished her classes and planned to attend a football game after school. Her classmates saw her speaking for several minutes to a man in a vehicle on Winchester Boulevard. One of the witnesses said the man was dressed like an ex-serviceman and wanted someone to babysit his sister's children for the afternoon. Thora got into the vehicle with him. She has never been heard from again.
After his discharge from the hospital, McGonigle was arrested by FBI agents. Several of Thora's classmates identified him as the man she was speaking to on the afternoon she disappeared. He was not an ex-serviceman, but admitted having stolen a foot locker from a serviceman which contained the Navy-issue clothes and military medals he was wearing on the day of Thora's disappearance. The foot locker was later found in the garage of McGonigle's home in San Mateo, California.
In one of his statements, McGonigle said he'd shot Thora accidentally while she was in his vehicle and she bled on the car's padding and upholstery, which he ripped out and buried. FBI agents later recovered it from its burial site in a drainage ditch near McGonigle's workplace; it was stained with human blood. There was also a bullet hole in the door of McGonigle's car, which was consistent with his statement. He said he'd removed the bullet from the door and buried it under a certain tree in his yard; the FBI found it there and determined it had in fact been fired from McGonigle's .32-caliber Colt revolver.
McGonigle gave several different accounts as to how he had disposed of Thora's body. At one point he said he'd thrown Thora's body off a steep 350-foot cliff known as the Devil's Slide, which overlooks Half Moon Bay on the San Mateo County coast. When police searched the area, they found Thora's two pairs of red and blue socks wedged in two different crevices partway down the cliff face. Her parents identified them. McGonigle had been working at a construction site at the time of his disappearance, and he got permission from his boss to fill in a nearby ditch with concrete blocks and dirt. When FBI agents dug up the ditch, they found Thora's shoes, schoolbooks and papers, binder and cowbell. McGonigle told investigators he'd buried her clothes in his backyard, but an excavation of the yard turned up nothing; no further trace of Thora was located.
McGonigle was charged with Thora's murder in spite of the fact that her body had never been found. Prosecutors theorized he killed her after she resisted his sexual advances, and her body was carried out to sea after he tossed it off the Devil's Slide. The jury deliberated only 38 minutes before convicting him. He also confessed to the murder of a San Francisco, California woman, but authorities decided not to charge him because he was already under sentence of death. At one point he claimed he had killed eleven people, but this could not be verified. In his last statment prior to his execution in the gas chamber in 1948, McGonigle claimed he was completely innocent of any involvement in Thora's disappearance.
Thora's body has never been found. Foul play is suspected in her case due to the circumstances involved.