San Francisco was first mentioned by Annabeth Chase when she told Percy Jackson how her dad was planning to move there for his studies. When he asked why she was so reluctant, she told him that every demigod should know that San Francisco is the most dangerous place a half-blood could be. Thalia Grace later explained to Percy that San Francisco was where the Mountain of Despair lies (which is why the Mist is so strong), and where many monsters dwell. Zoë Nightshade, Thalia, and Percy had to visit San Francisco and seek help from Annabeth's father, Frederick Chase, to get them to the mountain.
When Annabeth, Tyson, Percy, and Grover Underwood enter the Labyrinth, they emerge on Alcatraz Island on San Francisco. They save Briares, a hundred-handed one, but the prison was also where Kampê was. Percy mentioned that the Mountain of Despair had dark storm clouds swirling around it, saying that there was huge trouble brewing.
When Jason Grace, Piper McLean, and Leo Valdez are transported to a sidewalk cafe there by Aphrodite, they all went to Mount Diablo in San Francisco to find Piper's father, Tristan McLean, and fight Enceladus. It is also mentioned that Camp Jupiter is located there, the other reason why Greek demigods were warned not to go to, live in, or even be near this area.
Having been swapped with Jason Grace and his memory stolen by Hera, Percy meets Lupa at the Wolf House and he is told to use his senses to find Camp Jupiter. For three days, Percy had been chased and attacked by the Gorgon sisters, Euryale and Stheno after they met at a Bargain Mart.
Despite the area being a huge danger to demigods, Annabeth stays there during the school semester, but she did mention she was attacked by a lot of monsters during that time.
The San Francisco Bay area is home to Camp Jupiter, located east of Berkeley, west of Mount Diablo, south of Berkeley Hills, and north of Oakland Hills.