Officer Flanagan, 39, was shot and killed by a known robber and swindler named Spencer, who had been in the neighborhood of West 14th for several days, and had been annoying the women and children in the area. The suspect had been staying with the J. Cox family, at 502 West 14th Street, but refused when was asked to leave. The suspect refused the leave.

Officer Flanagan was investigating the complaints when he noticed Spencer standing in front of 502 West 14th Street. Spencer went inside the building, and Officer Flanagan followed him. As Officer Flanagan entered, with the intention of placing Spencer under arrest, he was shot. The two men then fired at each other inside the residence, until both were fatally wounded.

Officer Flanagan joined the department June 13, 1900, serving for three years until his death.