On January 5, 2006, the San Joaquin Joint Powers Authority—the agency managing the Gold Runner train between Oakland and Bakersfield—introduced a new Thruway route between San Jose and Merced via Gilroy and Los Banos. This route reduces travel time by two hours compared to the previous bus connection between San Jose and Stockton via the Altamont Pass, offering a total southbound travel time of about 6 hours and 30 minutes between San Jose and Los Angeles, and over 9 hours for northbound trips from LA to San Jose. Although still slower, this option makes the bus-to-train-to-bus connection more competitive with intercity buses that travel directly down I-5.

The route is open to all riders, and a train connection is not required. As a result, residents of Los Banos now have access to Silicon Valley, where intercity bus connections were previously lacking. Additionally, Silicon Valley residents can use the bus to reach Yosemite National Park by transferring to the YARTS bus in Merced, without needing to transfer to a train.