For decades you could see them from across the bay — two giant white “golf balls” atop Mount Tamalpais. Many residents knew they had something to do with the military, but the secrecy that initially surrounded them created rumors that persisted long after they had served their purpose.

So what exactly was perched on the west peak of Mount Tam, hiding in plain sight? A trip to The Chronicle’s archives had the photo negatives that could solve the mystery. And, indeed, Chronicle reporters had been the first to explain what was going on.

Even though many in the area knew of the base, built in 1951, the Air Force would only admit there was a radar “on a hill near Mill Valley.”

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In 1953, President Dwight Eisenhower pushed for more transparency, and the installation, officially called Mill Valley Air Force Station, was one of many projects declassified. The Chronicle pushed for access, and the Air Force allowed reporter Jack Foisie and photographer Bob Campbell inside the “nerve center” of the installation.

“BAY RADAR SECRETS TOLD,” shouted The Chronicle’s front page on Dec. 14, 1953.

Readers learned the radar station was part of a “network of posts” on both coasts that served as an “unbroken warning system against a surprise atomic punch by air.” The Air Force boasted the station was linked to Hamilton Field, 10 miles away near San Rafael, where fighter jets could be mobilized in seconds against “any unfriendly planes.” (The Cold War was ever-present — the same day’s front page included “Balky Yank” prisoners of war in Korea who wanted to stay and the California Medical Association approving a congressional investigation into communist sympathies in schools.)

The white domes were the most visible part of the station. Made of nylon and rubber, and supported only by internal air pressure, they provided weather protection to the radar antenna. Inside the station, personnel monitored the radar’s 200-mile range on a large Plexiglas board.

Although the threat subsided, the base stayed active until 1983. In 1973, The Chronicle interviewed the new base commander, Lt. Col. Wayne Mashburn. Mount Tam was generally regarded as “good duty” among Air Force officers. “But some people don’t like the 10-mile drive up the narrow twisting road.”

Weather at the peak could be an issue for the Air Force, as Mashburn described winds topping 80 mph ripping shingles from the buildings. There was also a surprise for Air Force officers expecting a more urban experience stationed so close to a major city. “Rattlers, in San Francisco?” was Mashburn’s response when he was first warned of scorpions and poisonous snakes near the station.

The base was abandoned by the Air Force as technological changes made the site obsolete. But the ruins of the base frustrated both the Marin Water District and the National Park Service, which inherited the land, for more than a decade, as columnist Carl Nolte described in a 1993 story.

“West of the domes, scattered over 100 acres, are 40 buildings — barracks with broken windows, a mess hall in ruins, a swimming pool full of dead leaves, cracked basketball courts, a tennis court that still has a sagging net, a ghostly movie theater, hobby shop, a sauna, and a row of small homes that once housed families,” Nolte wrote. Neither the Park Service nor the water district had the funds to clean up the base’s major asbestos problem.

The buildings were finally demolished in 1996. But before the “golf balls” disappeared off Mount Tam, they had a visitor who intended to use them for a more peaceful purpose.

On Oct. 10, 1989, the Dalai Lama — who had won the Nobel Peace Prize just days before — and an entourage took three helicopters to the peak, meeting about “a thousand invited guests, journalists and other ticket holders” for a private mountaintop ceremony at the former base.

Many abandoned “BMWs and Volvos at makeshift parking spaces on the winding road leading up Mount Tam,” Chronicle religion writer Don Lattin wrote. “Some less affluent pilgrims who camped out all night to get a glimpse of the Dalai Lama were chased off the mountain by park rangers.

“Perched atop a translucent sea of fog,” Lattin wrote, the Dalai Lama and a band of monks “performed ancient rites designed to create harmony between the people and their environment” and “turned an abandoned Air Force radar station into a Tibetan temple of peace.”

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•A fresco Red Scare: How Coit Tower’s murals became a target for anticommunist forces.

•$100 for a Jeep? The post-World War II military surplus and the Bay Area’s great Jeep rumor.

•When the pope visited San Francisco: Peter Hartlaub takes a look at the visit of another holy leader to the city — Pope John Paul II — with vintage popemobile shots.

From the Archive is a weekly column by Bill Van Niekerken, the library director of The Chronicle, exploring the depths of the newspaper’s archive. It’s part of Chronicle Vault, a twice-weekly newsletter highlighting more than 150 years of San Francisco stories. It is edited by Taylor Brown, The Chronicle’s newsletter editor. Sign up for the newsletter here, and follow Chronicle Vault on Instagram. Contact Bill at bvanniekerken@sfchronicle.com and Taylor at taylor.brown@sfchronicle.com.