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In 1986, the SFPD was responsible for investigating the disappearance of Gillian Taylor as well as the kidnapping of a patient from Mercy Hospital. Detective Chizum was placed in charge of both investigations and determined that people from the future were involved and put the case on the inactive list because he couldn't tell his superiors. (TOS short story: "Whales Weep Not")
In 2237, in an alternate reality, the SFPD investigated a series of killings perpetrated by an entity who became known as the Doctor. This was the first case on which Harve Bogenn worked as a junior-grade detective. The SFPD was stymied by the lack of physical evidence. In 2255 the Doctor reappeared in San Francisco, and Bogenn was again assigned to the case. When the Transamerica Pyramid was determined to be the Doctor's hideout, Bogenn and a SWAT team led by Captain Detroit responded to the building, but were convinced to allow Cadet James T. Kirk and Dr. Leonard McCoy to confront the killer. (TOS - Starfleet Academy novel: The Delta Anomaly)