The commute line between San Francisco and San Jose was one of the oldest rail corridors in California, predating the automobile era that would eventually diminish its ridership. Southern Pacific operated the service, running trains south through Millbrae, San Mateo, Palo Alto, and on to San Jose. The Third and Townsend Depot was the San Francisco end of this line, located in the city's SoMa neighborhood close enough to the Financial District for commuters to walk or transfer to streetcars. The depot never received a rail connection to the Transbay Terminal on the Bay Bridge, a missed opportunity that would have linked the Peninsula line to the East Bay rail system.

When Caltrain succeeded Southern Pacific's commuter service, the Third and Townsend location eventually gave way to the current terminus at Fourth and King Streets, about half a mile south. The old depot's location in what was then an industrial neighborhood has since been transformed by the South of Market development boom. Where rail passengers once arrived at a modest station surrounded by warehouses and light industry, AT&T Park (now Oracle Park) and a cluster of mixed-use developments now define the neighborhood's character. The depot itself was demolished, leaving no physical trace of the station that once connected San Francisco to the rest of the Peninsula.

The Third and Townsend Depot's story is partly about what did not happen. A direct rail connection between this station and the Transbay Terminal was never built, despite the obvious logic of linking the Peninsula commute line with the East Bay rail system on the Bay Bridge. Had that connection been made, San Francisco might have developed a unified rail network decades before BART provided the transbay link via tunnel. Instead, Peninsula commuters arriving at Third and Townsend and East Bay commuters arriving at the Transbay Terminal remained on separate systems, connected only by the city's surface transit. The depot's limitations shaped the fragmented transit geography that San Francisco lives with today.