Johnston spent the summer after college in the San Juan volcanic field of Colorado working with volcanologist Pete Lipman in his study of two extinct calderas. This work became the inspiration for the first phase of his graduate work at the University of Washington in Seattle, in which he focused on the Oligocene Cimarron andesitic volcanic complex in the western San Juans. Johnston's reconstruction of the eruptive history of the extinct volcanoes prepared him to study active volcanoes. Johnston's first experience with active volcanoes was a geophysical survey of Mount Augustine in Alaska in 1975. When Mount Augustine erupted in 1976, Johnston raced back to Alaska, shunting his former work on the Cimmaron Volcano into a master's thesis, and making Mount Augustine the focus of his Ph.D. work. He graduated in 1978 with his Ph.D., having shown that (1) the emplacement mechanism of the pyroclastic flows had changed over time, as they became less pumaceous, (2) the magmas contained high quantities of volatile water, chlorine, and sulfur, and (3) underground mixing of the felsic (silicic) magmas with less-viscous mafic (basaltic) magmas could have triggered eruptions. Mount Augustine was also the site of an early near-disaster for Johnston, when he became trapped on Augustine Island as the volcano was building toward another eruption.