A New York-based firm, sponsored by the commission, submitted plans for an expansive rapid transit system in 1956. In 1951, California's legislature created the San Francisco Bay Area Rapid Transit Commission to study the Bay Area's long-term transportation needs. An Army-Navy task force concluded that an additional trans-bay crossing would soon be needed and recommended a tunnel however, actual planning for a rapid transit system did not begin until the 1950s. Proposals for the modern rapid transit system now in service began in 1946 by Bay Area business leaders concerned with increased post-war migration and growing congestion in the region.

The final passenger run occurred on April 20, 1958 and the entire system was soon dismantled in favor of automobiles and buses and the explosive growth of highway construction.

This early twentieth century system once had regular transbay traffic across the lower deck of the San Francisco–Oakland Bay Bridge. Much of BART's current coverage area was once served by the electrified streetcar and interurban train network called the Key System. A 1915 study prepared for the cities of Oakland and Berkeley called a rapid transit link between the two cities 'imperative,' suggesting new street railway lines or an elevated railway between the two cities. There were also plans for a third-rail powered subway line ( Twin Peaks Tunnel) under Market Street in the 1910s. The idea of an electric rail tube under San Francisco Bay was first proposed in the early 1900s by Francis 'Borax' Smith – the San Francisco Chronicle ran a front-page editorial in 1900 suggesting an electrified subway. This map from 1960 included service through the Caltrain right of way as well as the Twin Peaks Tunnel, currently used for Muni Metro service, in addition to a Geary Subway and the constructed route down Mission Street (truncated to Balboa Park in this plan). BART was intended to take over existing rail corridors as well as incorporate new routes into the regional system. Envisioned master plan for rapid transit in San Francisco.

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