The Erlenmeyer Flask: Season 1 Episode 24 

Deep Throat directs Mulder to a crime scene where police are looking for a suspect who evaded capture and jumped into the river near an industrial area where Mulder & Scully find the case is being covered up.
Keywords: x-files, mulder, scully, full episode, the x-files, season 1, episode 24, the erlenmeyer flask