Although the site of the first California mission (1769) was on Presidio Hill by present-day Old Town, in 1774 Padre Junípero Serra moved it about 7 miles upriver, closer to water and more arable land, now the Mission Basilica San Diego de Alcalá. In 1784 missionaries built a solid adobe-and-timber church, which was destroyed by an earthquake in 1803. The church was promptly rebuilt, and at least some of it still stands on a slope overlooking Mission Valley.
With the end of the mission system in the 1830s, the buildings were turned over to the Mexican government and fell into disrepair. Some accounts say that they were reduced to a facade and a few crumbling walls by the 1920s. Extensive restoration began in 1931. The pretty white church and buildings you see now are the fruits of that work.
The mission sits north of an unlovely stretch of shopping centers and hotels along I-8 (take the Mission Gorge Rd exit); or take the San Diego Trolley Green Line to Mission San Diego, cutting through a scenic corridor not seen from the freeway.