Howard Gordon, portrayed by Scott Adsit, was a forensics scientist for the San Francisco Police Department.

In 2003, he showed Captain Stottlemeyer and Adrian Monk a dismembered torso that had washed up on the shores of San Francisco Bay (which was later identified as belonging to Larisa Zariyeva). While he was engaged in a scrutiny of the corpse, he failed to notice Monk obsessively cleaning crumbs off a computer keyboard, until it was too late to stop him from deleting years of forensic records.

In 2004, while investigating the murder of supermodel Clea Vance, Gordon identified the DNA samples from the scene as belonging to her boss, Julian Hodge. However, instead of doing his job, he met with Hodge in private, and offered to bury the case in exchange for a bribe. He and Hodge also plotted to frame Pablo Ortiz, a delivery boy, for the crime by falsely labeling samples taken from Pablo as those from the crime scene.

A few months later, he was planning to retire, explaining his ill-gotten gains as a lucrative payoff from a real estate investment. Monk became suspicious that someone may have tampered with the DNA evidence, so he and the SFPD duped Gordon into analyzing "newly discovered" DNA evidence from the crime scene. In actuality, the DNA evidence was actually planted, to test if Gordon was innocent. Gordon didn't analyze the DNA evidence (since he knew full well that it would identify someone other than Pablo, probably Hodge, as the killer), but stated under oath that it belonged to Pablo. This proved to be a very big mistake, as it confirmed to the police that he had switched the labels. They were also able to trace the bribe from Hodge.

Gordon was placed under arrest, and presumably imprisoned, as was Hodge. Pablo, meanwhile, was exonerated and released from prison.