Before Season 1Edit
Mueller was riding a moped in Berlin when he was killed after an ambulance crashed into him. A few weeks after his death, SD-6 found some of Mueller's plans at an FTL cover station and sent Antonio Quintero to the building to find them (Truth Be Told).
Season 5 Edit
During his time as a fugitive, Vaughn reveals to Sydney that he was familiar with Mueller before he'd heard about him from Sydney, and that he'd known him as the alleged originator of the Prophet Five project.