In 1985, Stoffel was recruited by the Office of Naval Intelligence (ONI) to work on missile technology. In his first year at ONI, his coworker, Jonathan Pollard was arrested for espionage. Stoffel openly despised dishonesty and repeated for years that Pollard was a money grubber who used spying for Israel as a way out. In 1987, he was part of the ONI team that proved that the USS Stark was hit by two missiles, which made it difficult for the Iraqis to claim a single accidentally fired missile was responsible.