Complex sentence: Its vision includes a new four-bore Transbay Tube beneath San Francisco Bay that would run parallel and south of the existing tunnel and emerge at the Transbay Transit Center to provide connecting service to Caltrain and the planned California High Speed Rail (HSR) system.
Split into simpler sentences: Its vision includes a new separate four-bore Transbay Tube beneath San Francisco Bay that would run parallel to and south of the existing tunnel. The new tunnel would emerge at the Transbay Transit Center to provide connecting service to Caltrain and the planned California High Speed Rail (HSR) system.