Emperor Norton's proclamation was easy to dismiss, but the idea refused to die. In October 1920, Major General George Washington Goethals -- the engineer who had built the Panama Canal -- proposed an underwater tube from the foot of Market Street to the Oakland mole. His alignment was almost identical to the tunnel that would eventually be built. Goethals understood that the Bay's soft mud, far from being an obstacle, could actually work in the tube's favor: a structure resting on yielding soil would flex during an earthquake rather than snap. Competing proposals multiplied through the 1920s -- bridge-and-tunnel combinations, southern crossings, a dozen schemes to span the water. In 1947, a joint Army-Navy Commission recommended an underwater tube to relieve congestion on the Bay Bridge, which was only ten years old and already overwhelmed. But it would take two more decades of seismic studies, political wrangling, and a statewide vote before construction finally began.

The engineering bordered on the improbable. At the Bethlehem Steel shipyard on Pier 70 in San Francisco, workers fabricated 57 individual tube sections on land, each between 273 and 330 feet long. After the steel shells were completed, watertight bulkheads were fitted and concrete was poured to form walls 2.3 feet thick. Then each section was floated -- literally, like a ship -- towed into the Bay by a catamaran barge, positioned over a trench that had been dredged 60 feet wide into the Bay floor, and sunk. Divers connected each new section to the ones already in place, removed the bulkheads between them, and packed sand and gravel against the sides. Lasers guided the dredging with accuracy within three inches. The route had been deliberately chosen to avoid bedrock, so the tube would remain free to flex rather than concentrate bending stresses at rigid contact points. The final section was lowered into place on April 3, 1969. Five years of fitting out -- tracks, electrification, ventilation, an automated dispatch system that gave regulators fits -- followed before the first revenue train rolled through.

On the evening of January 17, 1979, an electrical fire broke out aboard Train No. 117 as it passed through the tube. Burning plastic filled the tunnel with toxic smoke. Lieutenant William Elliott, a fifty-year-old Oakland firefighter, died of smoke and fume inhalation while working to extinguish the blaze. Forty passengers and two BART employees were rescued by a train passing in the opposite direction -- an improvised evacuation that worked despite the chaos, not because of any coordinated plan. Both the Oakland and San Francisco fire departments criticized BART for refusing to relinquish control of the emergency to professionals trained for exactly this kind of crisis. The tube remained closed until April 1979, and when it reopened, the state utilities commissioner issued a warning that the order to resume service "does not in any way provide a guarantee of safe service." The hard lessons from that night drove the creation of NFPA 130, the national standard for transit fire safety that now governs rail systems across the country.

When the Loma Prieta earthquake struck on October 17, 1989, a train was passing through the tube. The operator reported feeling no motion. Inspectors cleared the tunnel in six hours, and with the Bay Bridge closed for a month -- a section of its upper deck had collapsed onto the lower -- the Transbay Tube became the only direct passage between San Francisco and Oakland. But the earthquake revealed vulnerabilities. Studies found that settling and seismic shifting had reduced the allowable movement of the tube's flexible joints from 4.25 inches to as little as 1.5 inches. A 2002 vulnerability study concluded that the fill packed around the tube could liquefy during a severe quake, potentially allowing the buoyant hollow structure to break free of its anchorages. Retrofitting has been ongoing for decades: compacting the surrounding fill to resist liquefaction, bolting 2.5-inch-thick steel plates inside the tunnel to brace against lateral movement, installing higher-capacity pumps in case the Bay finds its way in. The tube was built to flex. The question that keeps BART engineers working is whether it can flex enough.

Riders know the sound before they know the cause. As trains curve beneath the Bay Bridge, where the tube's route bends to cross under the western span near Yerba Buena Island, the noise inside the cars climbs to 100 decibels -- jackhammer territory. BART has acknowledged that the sound "has been compared to banshees, screech owls, or Doctor Who's TARDIS run amok." The concrete walls amplify everything. Meanwhile, above the tube, the Bay's shipping traffic poses its own quiet threat: anchors dropped by freighters can damage the anodes that protect the tube's steel shell from corrosion. In January 2014, a drifting freighter dropped anchor near the tube, prompting a twenty-minute shutdown while inspectors confirmed no damage. George Lucas once filmed the climactic escape scene of THX 1138 inside the unfinished tunnel, rotating his camera ninety degrees so that Robert Duvall appeared to climb vertically toward daylight through what was, in reality, a perfectly horizontal tube. The future holds a second crossing -- Link21, approved by BART's board in June 2025, envisions a new tunnel running parallel to and south of the original, this time carrying standard-gauge regional rail to connect with Caltrain and California High-Speed Rail.