The horseshoe-shaped inner basin of the San Francisco Peaks is a collapse caldera that formed prior to the extrusion of Sugarloaf Dome, at least 80,000+ years before the present. The collapse may have been triggered by a seismic event or small volcanic eruption; no juvenile volcanic materials have been found in association with the event according to Dr. Richard Holm (Northern Arizona University, retired).
Prior to collapse the summit elevation of San Francisco Mountain was roughly 16,000 above sea level. The maximum elevation today is 12,666 feet. The top 3,500 feet of this composite volcano was transported eastward as a debris-avalanche towards the present-day location of Sunset Crater.
Holm, R.F., 2000, Landslide preconditions and collapse of the San Francisco Mountain Composite Volcano, Arizona, into cold debris avalanches in Late Pleistocene, https://www.journals.uchicago.edu/doi/pdf/10.1086/382763
Bezy, J.V., 2003, A Guide to the Geology of the Flagstaff Area. Arizona Geological Survey Down-to-Earth Series DTE-14, 56 p. http://repository.azgs.az.gov/uri_gin/azgs/dlio/1540