At San Francisco's Transbay Transit Center, there would already be a bullet train station under the original proposal. However, dead-ending the HSR there would have many missed opportunities.

It is proposed that a Second Transbay Tube be built, connecting San Francisco Transbay to Oakland Jack London Square. The underwater section would be dual gauge to allow BART trains to use it during rush hour. There would also be new connecting tunnels to the ends of the existing Transbay Tube for BART trains to transfer between tunnels. The eastern portal of the new underwater crossing would be in the railyard just south of South Prescott.

From there to Jack London Square Station, only track upgrading and electrification would be required.

At Jack London Square, trains would dive back into a tunnel to Orinda. It would run under 5th Avenue, Park Boulevard, and Shepherd Canyon Road to mimimize passing through private land. From Eastport, it would curve smoothly back into Orinda, where it would emerge from the tunnel. The section between Orinda and Pleasant/Contra Costa Centre Station would use BART's right of way and be the same elevation, though on separate tracks. The room for new standard gauge tracks in the middle of CA-24 freeway can be made by widening the median, which is just as simple as narrowing the fast lane freeway inner shoulders on both sides.

Walnut Creek would be a main station where passengers could transfer between BART, Amtrak commuter rail, high-speed rail, as well as buses.

The new tracks would run on a viaduct parallel to the existing BART viaduct until Treat Boulevard, where it diverges. There would be a new station at Contra Costa Centre for commuter rail only, with a footbridge connecting it to Pleasant Hill BART station. Pleasant Hill/Contra Costa would be another significant intermodal hub, though not as major as Walnut Creek as it would not serve HSR trains.

From Contra Costa Centre to Pacheco, it would run on a viaduct centered over the median of Contra Costa Boulevard.

From Pacheco northwards, the viaduct would curve smoothly into the interchange of I-680 & CA-4. Then, it would continue centered over the median of the 680 until Mococo, where it would descend into the existing Mococo Wye.

This project would be expensive as it requires an extensive tunnel through the Berkeley Hills. However, it is justified as the route would have a very high ridership.

Currently, Amtrak's Capitol Corridor is unpopular just because it is slow and has a low frequency of trains. The relatively low speed is partly due to the sharply curved tracks along the Carquinez Strait. With the proposal, Amtrak would open the New Capitol Corridor, which would have much shorter headways, serving as a true commuter railroad like the Northeast Corridor. This would become NorCal's primary Amtrak line, making the old Capitol Corridor secondary. Additionally, the new HSR line directly linking Sacramento to San Francisco would integrate the Bay Area and Sacramento into one economy. The short travel time on the bullet train between Sacramento Valley and San Francisco Transbay would make commuting between San Francisco and Sacramento realistic. Additionally, Bay Area tech companies looking for cheaper leases could expand into Sacramento without having their employees move homes. Similarly, people could live in Sacramento and work in San Francisco, making Sacramento's home values rise. The wealthier future commuting Sacramento residents would also spend more there, helping Sacramento's local economy.

All reasons in the paragraph above explain why the new line would have a high ridership. The high ridership means that a healthy revenue would be made. That would be more than enough to pay back the construction costs in a relatively short time. Perhaps net profit could be made from the New Capitol Corridor, like the Northeast Corridor.