Chief Dinan was later forced to resign under a charge of perjury from Special Prosecutor Francis J. Heney. Biggy was selected to replace the corrupt Dinan.

Soon, the spreading stain of the Ruef scandals even reached Chief Biggy. In October 1908, ex-convict and Ruef bagman Morris Haas, on trial for his part in an extortion scheme, shot prosecutor Heney in open court. Heney survived his wounds, but Haas was not so lucky. He was found dead in his jail cell with a bullet in his head. The gun, a .22 calibre derringer, was found in his shoe.

Some newspapers charged that Biggy was in the pay of the Ruef gang, and had ordered Hass killed to keep his mouth shut about the attack on Heney. While Biggy vigorously denied the allegations, he considered resigning until he could clear himself. Only the strenuous arguments of Police Commissioner Hugo Keil, that resignation would be tantamount to a confession, persuaded Biggy to remain.

Biggy continued to consult with Keil about the status of the investigation into Haas' death. At sundown on the night of November 30, 1908, Biggy crossed the Bay on the police boat "Patrol," to talk to Keil at his Belvedere home. The two men discussed the Haas case until 11 o'clock that night and, according to Keil, Biggy had been persuaded to remain in office, and said the chief had been in a cheerful mood when he left Belvedere for the return trip to the city.

But Biggy never returned to San Francisco. Shortly after midnight, Biggy boarded the "Patrol" manned only by its pilot, a police officer named William Murphy, and cast off for the city. When the boat docked, Biggy was not aboard. Officer Murphy told waiting policemen that he had last seen Chief Biggy leaning against the rail as the boat passed Alcatraz.

A search party set out immediately for Alcatraz, but the night fog was thick, and the search was postponed until the next morning. Three days later, the searchers gave up. It wasn't until December 15 that the chief's body was found floating in the Bay, off the rocks of Angel Island.

Officer Murphy was taken into custody and questioned at length about the events of November 30, but stuck to his story. The coroner found no marks on Chief Biggy's body which would indicate a struggle.

Because Biggy, a devout Catholic, was considered an unlikely suicide; the Coroner's Jury returned a verdict of accidental death.

Newspapers had a field day. They speculated that like Haas, Chief Biggy knew too much about the Abe Ruef gang and had been killed to keep him from talking. But, if Ruef or a member of his organization had anything to do with the chief's death, they never revealed the secret.

The Sunday before Christmas 1908, the entire police department turned out for Chief Biggy's funeral at St. Mary's Cathederal on Van Ness Avenue. He was eulogized as "a faithful officer who has fallen in the line of duty."

The death of Chief Biggy was never solved, and the circumstances surrounding his disappearance and death remain a mystery.