Wait, We’ve Been Flying the Flag the Alitos Had? San Francisco Takes It Down.

It turns out that the New Jersey vacation home of Justice Samuel A. Alito Jr. was not the only surprising place where a provocative flag adopted by Jan. 6, 2021, rioters has flown recently.

For 60 years, residents in San Francisco could have spotted the flag in a public pavilion just a stone’s throw from the mayor’s balcony at City Hall. The “Appeal to Heaven” flag was among the 18 historic banners that billowed over a central plaza in one of the nation’s most liberal cities, where fewer than 13 percent of voters supported former President Donald J. Trump in the 2020 election.

Few people, including Mayor London Breed, made much of the white flag with a green pine tree. Until last week.

A San Francisco resident raised concerns that the “Appeal to Heaven” flag was flying over the city, after revelations in The New York Times that the same flag had flown outside Justice Alito’s second home on Long Beach Island, N.J. Critics said Justice Alito should have recused himself from cases related to the Jan. 6 attack because of the flag’s association with the rioters at the U.S. Capitol who attempted to stop the certification of Joe Biden as president.

Ms. Breed ordered the flag’s removal, and city employees replaced it on Saturday with an American flag, according to Jeff Cretan, a spokesman for the mayor. A bronze plaque that explained the history of the flag was also removed from the pole.

The flag dates to the Revolutionary War and was flown from George Washington’s ships as a symbol of rebellion against the British. Above the tree, the white flag has the words “An Appeal to Heaven” in black lettering. It has been adopted in recent years by conservatives seeking to inject Christianity into American government, as well as by supporters of Mr. Trump and the “Stop the Steal” campaign — efforts that are deeply unpopular in San Francisco.

“Our responsibility is to represent the values of our country and the city and county of San Francisco, and the values of our city and county aren’t aligned with those who tried to overthrow the government,” Mr. Cretan said on Thursday.

In a different era, San Francisco leaders had civic intentions when they installed the “Appeal to Heaven” flag on Flag Day in 1964. It was one of 18 hoisted in a historic exhibit that was dubbed the Pavilion of American Flags, which was intended to showcase flags that had played an important role in the country’s history.

Each flag was sponsored by a local nonprofit organization, and most of the original 18 have remained in place ever since. Nine flags fly from towering white poles on either side of a large pathway connecting the majestic City Hall and its signature gold dome with the Main Library and the Asian Art Museum across the plaza.

“There’s a difference between choosing to raise the flag in this moment and the flag being a longstanding part of a historic exhibition,” Mr. Cretan said.

Justice Alito has faced criticism not just because of the “Appeal to Heaven” flag but also because his home in Virginia displayed an inverted American flag weeks after the Jan. 6 attack — a symbol of distress that was also adopted by Trump supporters. Justice Alito on Wednesday defended his decision not to recuse himself from two cases stemming from the Capitol attack because he said he had “nothing whatsoever” to do with the flags, which he said had been displayed by his wife, Martha-Ann.

It may surprise people to hear that San Francisco has continued to fly the “Don’t Tread on Me” flag — a yellow banner with a black, coiled rattlesnake that was also a symbol of defiance against Britain during the Revolutionary War. It became a symbol of the conservative Tea Party movement about 15 years ago and has been criticized by some as having racist connotations.

That flag also was carried by Trump supporters at the U.S. Capitol on Jan. 6, 2021.

Mr. Cretan said that flags and symbols changed over time and that the city would try to ensure the flags in Civic Center Plaza reflect current values. The mayor will decide whether other flags come down but will welcome input from others, Mr. Cretan said.

The San Francisco exhibit mostly contains iterations of the American flag, on which stars were added as states joined the union. It also includes the California flag and the Texas Lone Star flag. Flags that today’s San Franciscans might feel more affinity for — like the rainbow Pride flag supporting L.G.B.T.Q. rights — are not part of the display.

It is not the first time the pavilion has caused consternation in the city.

The original display included a Confederate flag, which flew until a protester scaled the pole and tore it down in 1984.

Dianne Feinstein, who was then the mayor of San Francisco, briefly allowed it to be replaced by another Confederate flag before removing it permanently. That episode was cited by progressive school board members as justification for removing Ms. Feinstein’s name from a local elementary school in 2021. They agreed to change the names of 43 other schools as part of the same effort targeting historic individuals they found offensive — including Abraham Lincoln High School.

Three of the board members were recalled in 2022 by voters who were frustrated by the renaming campaign and school closures during the pandemic. The name changes were dropped before the recall.

Ellen Schumer, the City Hall historian, said she was not surprised that nobody had raised objections to the “Appeal to Heaven” flag until last week. She used to train her docents on the meaning behind each flag for City Hall tours but stopped after realizing visitors did not seem to care about the flag exhibit.

“I guess if you’re a flag collector,” she said. “Other than that, there’s no interest.”

On Thursday, children played on the playgrounds at the Plaza, a man in workout gear did tai chi, and people in suits were buried in their phones as they rushed to their offices. Few seemed to glance at the flags, and security guards in the plaza said they had never thought about the banners one way or the other.

Instead, the focus was on preparing Civic Center Plaza for a very different sort of event: a Saturday night rave featuring two D.J.s, Skrillex and Fred Again, that is expected to draw 20,000 revelers under the flags.