Congresswoman Jackie Speier, then serving as a California State Senator, is credited with securing the funding for CTX and one of the new locomotives acquired for the project is named for her as a result.

On September 21, 2024, with the completion of the Caltrain modernization project and the transition to electrified trains, the Baby Bullet was renamed as simply the Express service.

[1] In 1997, after plans to extend Caltrain to downtown San Francisco were put on hold, the Peninsula Corridor Joint Powers Board (PCJPB) started the Rapid Rail Study, which was published as a draft in October 1998.

[2] Proposed rehabilitation work included rebuilding tracks and grade crossings to enable Caltrain to raise the systemwide speed limit to 79 to 90 mph (127 to 145 km/h) and replacing bridges, culverts, and signals.

[2] In 1999, PCJPB published an implementation plan for the Rapid Rail Study which called for a $280 million investment from the three counties served by Caltrain.

[4] Senator Speier sponsored Senate Bill 2003 in February 2000 authorizing US$127,000,000 (equivalent to $218,500,000 in 2023) to fund CTX;[5] the first draft of the bill included funding to create "little bullet" express Caltrain service between San Francisco and San Jose (with the goal to cut transit time in half compared to local, all-stop service) and also to rehabilitate the Dumbarton Rail Bridge in preparation to reroute Altamont Corridor Express (then Altamont Commuter Express) service from Stockton over the Dumbarton Rail Corridor.

[12] The groundbreaking was attended by officials and politicians who had supported CTX, including Senator Speier, Governor Gray Davis, Secretary of Transportation and Housing Maria Contreras-Sweet, MTC Commissioner Sue Lempert, Caltrans Director Jeff Morales, and San Mateo County Supervisor Mike Nevin.

[12] During CTX construction, Caltrain shut down weekend service for two years starting in July 2002 to allow track work.

[20] Construction was substantially complete by May 2004 when Caltrain began running "test" trains on the weekends to shake down the system and gain crew experience,[17][21] and the Baby Bullet trains entered revenue service on June 7, 2004; the first northbound Baby Bullet discharged over 600 passengers upon its arrival in San Francisco at 6:45 a.m., and had carried more than 1,000 during its inaugural run.

[24] In addition to having one of the new locomotives named for her, Senator Speier received MTC's John F. Foran Legislative Award for her pivotal role in bringing Baby Bullet service online.

[30] The key elements of CTX were the overtake tracks, high-speed crossovers, and a central traffic control system which collectively allowed a single office to route trains.

The new T Third Street line, which opened in 2007, terminates at Sunnydale Station as Muni Metro has never built any tracks in San Mateo County, and a planned 0.5-mile (0.80 km) loop extension to Bayshore was studied in 2012.

[13][22][39] This cuts my commute so much that it's faster than driving.The revised schedule was the product of more than two hundred iterations, and added ten trains per weekday without increasing staffing because equipment was being used more efficiently.

[57][62] There were four weekend/holiday Baby Bullets per day (two in the mornings and two in the evenings), each making seven intermediate stops between 4th&King and Diridon: Millbrae, San Mateo, Hillsdale, Redwood City, Palo Alto, Mountain View, and Sunnyvale; these stations were selected for their proximity to activities as probable leisure time destinations.

[52] Caltrain service on weekends north of Bayshore was suspended and replaced by a bus bridge from October 2018 to March 2019 in order to accommodate tunnel notching work for the Peninsula Corridor Electrification Project.

Weekend Baby Bullet trains originated and terminated at Bayshore, and a bus bridge made stops at both stations in San Francisco.

[63] Weekday Baby Bullet service was restored on August 30, 2021, with twelve trains total: six northbound and six southbound, with three each during peak morning and afternoon commute hours.

[70] During the first year of Baby Bullet service in 2004, the five-car Bombardier consists had a capacity of only sixteen bicycles per train, and carried heavy passenger loads.

The MP36PH-3C locomotives and BiLevel Coaches remain in service, now exclusively serving the South County Connector between San Jose Diridon and Gilroy.