The 1906 San Francisco Earthquake and fire destroyed most of San Francisco in 1906 due to poor city planning and substandard building materials. Poor organization further hindered recovery efforts. The survivors rebuilt the city in a much more organized fashion. Another major quake occurred between 2008 and 2374 and the city fared much better. (ST - New Worlds, New Civilizations short story: "At Times of Peril")
The maintenance culverts in the Presidio survived the earthquake. In 2255, in the Kelvin timeline, Cadet James T. Kirk was led through the culverts by the Gemini Project neural agent with which T'Laya infected him. (TOS - Starfleet Academy novel: The Gemini Agent)
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