The Neogene stratigraphic and tectonic history of the Mount Diablo area is a consequence of the passage of the Mendocino Triple Junction (MTJ) by the San Francisco Bay area between 12 and 6 Ma, volcanism above a slab-window trailing the MTJ, and crustal transpression beginning ~8-6 Ma, when the Pacific Plate and Sierra Nevada microplate began to converge obliquely. Between ~12-6 Ma, parts of the Sierra Nevada microplate were displaced by faults splaying from the main trace of the San Andreas Fault and incorporated into the Pacific Plate. The Mount Diablo anticlinorium was formed by crustal compression within a left-stepping, restraining bend of the eastern San Andreas Fault system (SAF), with southwest-verging thrusting beneath, and with possible clockwise rotation between faults on its southeast and northwest. At ~10,5 Ma, a drainage divide formed between the northern Great Central Valley (GCV) and the ocean. Regional uplift accelerated at ~6 Ma with onset of transpression between the Pacific and North American plates. Marine deposition ceased in the eastern Coast Range basins as a consequence of the regional uplift accompanying passage of the MTJ, and trailing slab-window volcanism. From ~11 to ~5 Ma, andesitic volcanic intrusive rocks and lavas were erupted along the northwest crest of the central to northern Sierra Nevada and were deposited on its western slope, providing abundant sediment to northern Great Central Valley (GCV) and the northeastern Coast Ranges. Sediment filled the GCV, overtopped the Stockton fault and arch forming one large, south-draining system that flowed into a marine embayment at its southwestern end, the ancestral San Joaquin Sea. This marine embayment shrunk with time and by ~2.3 Ma was eventually cut off from the ocean. Fluvial drainage continued southwest in GCV until it was cut off in turn, probably by some combination of sea level fluctuations and transpression along the SAF that uplifted, lengthened and narrowed the outlet channel. As a consequence, a great lake, Lake Clyde, formed in the GCV at ~1.4 Ma, occupying all of the ancestral San Joaquin Valley and part of ancestral Sacramento Valley. The lake rose and fell with global glacial and interglacial cycles. After a long, extreme glacial period, Marine Oxygen Isotope Stage (MOIS) 16, it overtopped Carquinez sill at 0.63 Ma and drained via San Francisco valley (now Bay) and the Colma gap, into the Merced marine embayment of the Pacific Ocean. Later, a new outlet for GCV drainage formed between ~75 and ~130 ka ago., when the Colma gap closed due to transpression and right-slip on the SAF, and Duxbury Point at the south end of Pt. Reyes Peninsula moved sufficiently northwest along the SAF to unblock a bedrock notch, the feature we now call the Golden Gate.