Navy subs, nuclear secrets and beer: The riveting history of Bay Area’s Mare Island

If you’ve ever watched the 2023 movie “Oppenheimer,” there’s a scene where the titular physicist watches soldiers put bomb parts into trucks that then drive off into the horizon. Everyone knows what happened after that: The U.S. dropped the atomic bomb on Japan, leading to the end of World War II and the advent of the nuclear age.

What isn’t shown is those bomb parts reportedly first headed to Mare Island, a ship-building facility in Vallejo in the northern San Francisco Bay.

“These packages came into a small building. Nobody knew what was in them. There were armed Marines on all the rooftops around it, basically snipers,” says Kent Fortner, president of the Mare Island Historic Park Foundation. “If you talk about the seminal event of the world in the last century, it might be the dropping of the atomic bomb. All that came to pass through right here on the island.”

This gripping nugget is among hundreds from Mare Island — despite its name, it’s technically a peninsula — whose secrecy-shrouded past dates from the Civil War to its decommissioning in the 1990s. More than 500 numbered vessels were built here, and a thousand-plus more overhauled. The first commander was Admiral David Farragut of “damn the torpedoes, full steam ahead!” fame. Mare Island supported the Navy during both world wars and helped spy efforts during the Cold War by using nuclear submarines to tap Soviet cables.

Mare Island Historic Park Foundation board member Jim Reikowsky, center, leads a tour group through St. Peter’s Chapel at Mare Island on Wednesday, Feb. 19, 2025, in Vallejo, Calif. (Aric Crabb/Bay Area News Group) 

Even if you don’t know about its past, it’s a fascinating place to visit. Almost 3.5 miles long, it has a mix of residential blocks with neocolonial homes and an industrial waterfront on the Napa River with functioning dry docks and “Star Wars”-scale cranes. There are scenic hiking areas and a lovely park, featuring concrete bomb shelters and a nuclear Polaris missile aimed at the sky. Then there are the commercial enterprises that moved in once the Navy left – art studios, tasting rooms for wines and whiskey and a brewery pouring Navy-themed suds in an old coal shed.

On a recent afternoon, Lew Halloran is leading a tour of the same place he was stationed as a Navy man from 1989 to 1993. Mare Island’s historic foundation offers these public tours as part of its educational programming, along with a speaker series with topics like the advent of kamikaze pilots and 2,000 years of cryptography.

“The purpose of Mare Island was to maintain ships and to build ships. That’s why she’s here. And by the time we came up to closure, this yard could do anything,” says Halloran.

He gestures around: There was a shop for bending and X-raying pipes and a foundry to cast propellers. A sawmill and a place to calibrate periscopes. A coffee roaster and grinder that did nothing during World War II but make 5-pound coffee cans for caffeine-deprived sailors. A paint factory and laboratory where research against barnacles supposedly led to superglue. There were craftsmen who could fix your wooden leg.

“They could tear apart a boiler and put it together again from scratch,” says Halloran.

Nearby, a siren suddenly blares. Foghorn blasts and electronic shrieks around the base give the uncanny impression the Navy never left.

“I don’t know what that means,” he frowns. “Nobody’s running, so I think we’re good.”

A then-restricted photo from 1945 shows a warship at the Mare Island Naval Shipyard in Vallejo, Calif. (Mare Island Historic Park Foundation)
A then-restricted photo from 1945 shows a warship at the Mare Island Naval Shipyard in Vallejo, Calif. (Mare Island Historic Park Foundation) 

Mare Island’s bellicose history goes back to its name. A Californio general lost his prized horse overboard in 1835 and later found it wandering the peninsula – thus “Isla de la Yegua” or Island of the Mare. During the Gold Rush, the U.S. government carved out land here to protect the San Francisco harbor and its booming economic activity. The first ship built was the USS Saginaw in 1859, a paddle-wheel gunboat used in the Civil War to guard against Confederate marauders.

Admiral Farragut assumed control in these early years with the intention of nurturing a world-class shipyard on the lines of what existed on the East Coast. Things began gaining momentum in the early 1900s, when the yard teamed up with Union Iron Works in San Francisco for armored ships, built ahead of schedule and under cost. Churning out destroyer escorts and submarine chasers elevated operations during World War I, because German subs were sinking convoys left and right.

World War II saw employment surge through the roof. Ultimately, some 45,000 people worked here, a quarter of them women.

“They were building submarines, all kinds of destroyers, and interestingly enough the biggest need in terms of number of vessels were landing crafts,” says Dennis Kelly, a foundation board member who refilled nuclear submarine reactors here during the 1970s. “Mare Island built so many tank landing crafts that if you laid them out in row, it’d stretch for six miles.” (These vehicles’ parts were shipped by train from Colorado, and what determined their ultimate size was the size of a single railroad tunnel under the Continental Divide.)

A tour group looks over a canon on display in Alden park at Mare Island on Wednesday, Feb. 19, 2025, in Vallejo, Calif. (Aric Crabb/Bay Area News Group)
A tour group looks over a canon on display in Alden park at Mare Island on Wednesday, Feb. 19, 2025, in Vallejo, Calif. (Aric Crabb/Bay Area News Group) 

Mare Island was one of only two public shipyards in America that built nuclear submarines during the Cold War. It hosted an “ocean-and-engineering program” that actually was a highly classified mission called “Ivy Bells,” sunk deep in the Soviet Sea of Okhotsk.

“We had telephone taps that were 20 feet long and would take them by submarine with saturation divers to tap into undersea lines and record conversations,” Kelly says. The tapes were swapped at Mare Island, then presumably flown in handcuffed briefcases back to D.C. for analysis. “That program was credited for helping end the Cold War, because we were very hawkish about what the Soviets were up to and found out they were actually more worried about us attacking them.”

Dry dock one at Mare Island on Wednesday, Feb. 19, 2025, in Vallejo, Calif. (Aric Crabb/Bay Area News Group)
Dry dock one at Mare Island on Wednesday, Feb. 19, 2025, in Vallejo, Calif. (Aric Crabb/Bay Area News Group) 

The base was decommissioned in 1996 when a federal cost-benefit analysis of military bases found it lacking for the post-Cold War age. There was a three-day “conversion” ceremony — the term “closure” seemed too grim — with river patrol boats from the Vietnam era and Marines jumping out of a helicopter. But there’s still plenty to explore today, and you don’t even need a top-secret pass.

St. Peter’s Chapel is the oldest standing Navy chapel in the United States, dedicated in 1901. It’s cozy, but the vaulted wood ceilings and Tiffany stained-glass windows lend a grand and Gothic air. Plaques pay tribute to every conflict the Navy’s been in, from the Revolutionary War to Vietnam, and are made from metal salvaged from notable ships — including the USS Hartford, which Farragut steered through withering fire from Confederate cannons in 1864’s Battle of Mobile Bay (“damn the torpedoes!”). Tour the chapel on the second and fourth Sunday of the month, or take a tour in which your guide may noodle on the old church organ.

Nature lovers might enjoy the Mare Island San Pablo Bay Hiking Trail, an easy walk near the water that should get you thirsty for a beer later. And budding botanists will delight in identifying the individually tagged trees all around Mare Island that hail from far corners of the world: Canary Island Pine, Chinese Pistache, Brazilian Pepper, Chilean Soap Tree.

Many of these owe their origins to Commodore James Alden in the late 1800s. “He told ship captains, ‘Wherever you go, pick saplings and send them back, and I’ll plant them here,” says Halloran. “As far as trees go, this island is supposedly the most biodiverse in the country.”

A tour group walks through Alden park at Mare Island on Wednesday, Feb. 19, 2025, in Vallejo, Calif. (Aric Crabb/Bay Area News Group)
A tour group walks through Alden park at Mare Island on Wednesday, Feb. 19, 2025, in Vallejo, Calif. (Aric Crabb/Bay Area News Group) 

The alien species have led to at least one close call, when a yard worker was clearing around an Australian bunya-bunya in the 1960s. “As I raked around the tree, I heard several loud noises coming from above me,” he recalls on a University of California gardening blog. “I looked up and at the same time, a cone hit the ground about 10 feet away from me. I took the cone home with me and weighed it. It weighed 20 pounds.”

The Mare Island Art Studios is a quirky collective of painters and sculptors located on the banks of the Napa River. It’s open to the public every Sunday afternoon, when visitors might meet a resident artist such as Jean Cherie. She’s working to decorate the ferry dock at the old base with a 10-foot bronze statue of Wendy the Welder, the lesser-known cousin of Rosie the Riveter.

“Somebody said there’s not really anything that represents the women who worked here during World War II. I said, ‘Yeah, I can fix that,’” says Cherie.

As you might imagine for a place filled with sailors, the drinking culture on Mare Island was robust in its day. Submariners who earned their “dolphins” – their hard-won insignia – couldn’t just pin them on. They had to first drop them into a pint glass filled with every liquor imaginable and drink it all the way down. There was a bar named Chesty’s in the former Marine Corps barracks. It was named after Lewis “Chesty” Puller, a famously hard-ass Marine given to wisdom like, “We’re surrounded. That simplifies the problem.” (By firing in every direction.)

A public artwork called Tonglen by artist Ryan Mathern is on display on Mare Island in Vallejo, Calif., on Sunday, March 2, 2025. (Jose Carlos Fajardo/Bay Area News Group)
A public artwork called Tonglen by artist Ryan Mathern is on display on Mare Island in Vallejo, Calif., on Sunday, March 2, 2025. (Jose Carlos Fajardo/Bay Area News Group) 

This drinking tradition lives on at the Vino Godfather Winery, which serves flights and charcuterie, and the new tasting room of Redwood Empire Whiskey, with its Sonoma-style bourbon and Southern menu designed by a real Kentucky colonel. Then there’s the Mare Island Brewing Co.’s Coal Shed Brewery, run by Ryan Gibbons and Kent Fortner – yes, the president of the Mare Island Historic Park Foundation.

The taproom is sheltered in a hulking shed formerly used to store coal for ships, including Teddy Roosevelt’s Great White Fleet, the battleships that circled the globe. When an electrician wired up the brewery, Fortner pointed him to a panel so big, it looked like its own room. “He’s like, ‘Oh my God – there’s enough power here to power a battleship,’ and comes to the realization that we had enough electricity to run a small city off these things because that’s what these ships were.”

The vehicle that took food around to the nearly 50,000 workers during World War II at the Mare Island Naval Shipyard in Vallejo, Calif. (Mare Island Historic Park Foundation)
The vehicle that took food around to the nearly 50,000 workers during World War II at the Mare Island Naval Shipyard in Vallejo, Calif. (Mare Island Historic Park Foundation) 

The brewing company pays tribute to the local history with beers like Chesty’s Barrel Aged Stout and the porter General Order No. 99, aged in a bomb shelter and named for the Navy Prohibition directive banishing alcohol from bases. For grub, there’s a food truck called the Pie Wagon serving hand pies, crab cakes and fries. It is named after a World War II-era, luggage-toting type of vehicle that delivered food to nearly 50,000 people on base.

“Mare Island is the most unique and awesome branding opportunity I’ve come across,” Fortner says. “It’s a story that desperately needs to be told. It’s one of most important places on the West Coast in terms of naval history, and it impacted the world in so many ways.”

That includes the small building used to store Oppenheimer’s atomic-bomb parts and which is no longer standing.

“There’s a taco truck that sits there where I eat about once a week,” says Fortner. “We call it the atomic taco truck.”

If You Go

Mare Island tours: The Mare Island Historic Park Foundation offers tours by reservation during the first and third weeks of each month at 10 a.m. Thursdays and Saturdays and 2 p.m. Sundays. Tours are $20 per person (children are free) and begin at St. Peter’s Chapel, 1181 Walnut Ave. in Vallejo. Find details and book a tour at www.mihpf.org/tours.

Mare Island Art Studios: Open from noon to 4 p.m. on Sundays at 110 Pintado St.; https://mareislandartstudios.com/.

Vino Godfather Winery: Open noon to 7 p.m. Thursday-Sunday at 1005 Walnut Ave.; www.vinogodfather.com/.

Redwood Empire Whiskey: This distillery tasting room on Mare Island is scheduled to reopen this spring; https://redwoodempirewhiskey.com/.

Mare Island Brewing Co.: The Coal Shed Brewery taproom opens at 11:30 a.m. Wednesday-Saturday at 850 Nimitz Ave.; www.mareislandbrewingco.com.



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