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(covers information from several alternate timelines)
San Francisco Bay was an estuary on the western coast of the North American continent on Earth. A strait connected this bay to the North Pacific Ocean. Within the bay, there were a small number of islands, including Angel Island and Treasure Island. (Star Trek IV: The Voyage Home) The cities that developed around this bay were known as the San Francisco Metropolitan Area. This area was in Earth Sector 2. (Star Trek Into Darkness)
In an alternate timeline the bay was visited in 1944 by Commander Charles Tucker III and Ensign Travis Mayweather in Shuttlepod 1 of the starship Enterprise NX-01. Unaware at first, that they had traveled into the World War II era in an alternate timeline, they found their shuttle under attack by a squadron of P-51 Mustang fighters and beat a hasty retreat. A substantial United States Navy Task Force was seen gathered in the bay. (ENT: "Zero Hour", "Storm Front")
In 2258 in the alternate reality, the Narada deployed its drilling platform over the inlet of San Francisco Bay, right next to the Golden Gate Bridge, and began drilling a hole toward Earth's core. The drilling platform was destroyed by Spock in the Jellyfish, its debris falling into the bay. (Star Trek)
In the alternate reality of 2259, a map of the San Francisco Bay was part of a collection of graphics and video media that were displayed on a powerwall in Admiral Christopher Pike's office. Within a few days, the USS Vengeance crashed into the bay, devastating both Alcatraz and San Francisco. (Star Trek Into Darkness)
In 2286, the captured Klingon Bird-of-Prey HMS Bounty crash-landed in the bay, due to the effects of the Whale Probe, but stayed afloat long enough to release the humpback whales George and Gracie. (Star Trek IV: The Voyage Home)