His second marshalship had elements consistent with the renegade nature of that era, when he was shot dead by one of his deputy officers over a quarrel regarding reward money.

As a deputy city marshal, at the end of 1861, Warren assisted J. E. Pleasants, overseeing one of William Wolfskill's ranches, to pursue and capture several horse thieves who were sent to the penitentiary.

[2] However the following year: During the second marshalship of William C. Warren, when Joe Dye, was one of his deputy officers, there was great traffic in Chinese women, one of whom was kidnapped and carried off to San Diego.

A reward of a hundred dollars was offered for her return, and she was brought back on a charge of theft and tried in the Court of Justice Trafford, on Temple Street near Spring.

At a spot near the corner of Spring and Temple streets Dye shot and killed Warren; and in the scrimmage several other persons standing near were wounded.