RICHMOND, Va. » One floor below street level in the Museum of the Confederacy here, at the end of a cinder-block hallway behind two sets of locked double doors, a climate-controlled vault contains the world’s largest collection of some of the most revered and reviled objects in U.S. history: Confederate-era flags.

Here, painstakingly preserved and cataloged, are more than 550 wartime silk, wool and cotton flags. One, fashioned from bridal clothes, has the word "Home" in blue appliqué, encircled with blue stars. Another features an oil painting of Pocahontas. Still another, the now-controversial Southern Cross battle flag, was once owned by Tad Lincoln, a son of the former president. It hangs in a gallery upstairs.

As the museum’s chief historian and author of a scholarly book on the flag, John M. Coski, a slender and slightly rumpled 56-year-old, works hard to bring its various versions to light — part of what he calls a "conscious effort" by officials of the 119-year-old institution to "modernize from a shrine" to the old South into "a modern, Smithsonian-like museum."

As debate rages over how and where to display Confederate flags — an issue the South Carolina General Assembly took up Monday — critics insist that they must be relegated to museums. But here in Virginia, it is clear that even museums cannot escape the fray.

"They like to hide theirs in the basement," said Grayson Jennings, a founder of the Virginia Flaggers, whose members were waving modern replicas of the battle flag recently to protest another Richmond museum, the Virginia Museum of Fine Arts, which in 2011 removed the flag from a Confederate chapel on its property.

Of the Confederacy museum, Jennings said, "Most of us real Southerners dropped their membership quite a few years ago."

Richmond, after all, was the capital of the Confederacy; the museum is adjacent to, and includes, the grand-columned Confederate White House where Jefferson Davis, the Confederate president, lived. Jennings and other flag defenders object to its merger with the much newer American Civil War Center, which opened in 2006 along the banks of the James River, on the site of the Tredegar Iron Works, the Confederacy’s major manufacturer of cannons and artillery.

The center tells the story of what old-school Southerners call the War Between the States — from Union, Confederate and African-American points of view. As it was being planned, said its founding president, H. Alexander Wise Jr., there was talk of joining with the Confederacy museum, which has a vast collection of artifacts, much of it gathered by women who solicited memorabilia from their families. The collection includes bullet-ridden uniforms, fragile letters and the sword Robert E. Lee used to surrender at Appomattox in 1865.

"But there was a point at which they wanted to edit the story, and control the story," said Wise, a onetime board chairman of the Confederacy museum and former director of historic preservation for Virginia. "And we said, ‘Nuh-uh, this is an overarching story.’"

With prodding from local philanthropists, the two institutions came to terms, and now operate on paper and the Internet as The American Civil War Museum. In 2017, a new joint exhibition hall will open on the Tredegar site.

B. Frank Earnest, a past commander of the Virginia division of the Sons of Confederate Veterans, is enraged.

"Everything in that museum was donated by people who are descendants of Confederate soldiers," Earnest said. "People donated believing that this was going to be a memorial to the Confederacy, and the Confederate soldier and the cause for which he fought."

But new times — and declining attendance — demand new ideas, museum officials say. Ed Ayers, a Civil War historian, president emeritus of the University of Richmond and chairman of the new museum’s board, argues the joint effort will reveal the war’s "power and its mystery" — and lead to greater understanding.

"Without that understanding," he said, "we will find ourselves perpetually confused and squabbling, as we have been for the last 150 years, and as we are today."

The venture (technically "a consolidation," not a merger) has two chief executives: a black museum specialist, Christy Coleman, 50, who led the Civil War Center; and S. Waite Rawls, 66, a white retired investment banker and descendant of Confederate soldiers, who ran the Confederacy museum. Both risked the wrath of donors, and neither is a stranger to tough questions about the flag.

"People ask me, ‘Why don’t you fly the Confederate flag?’" Coleman said. "I say, ‘Which one? Are we talking about the one with Pocahontas on it? Or are we talking about the one that has blue and white stars and says the word ‘Home’?"

When the Museum of the Confederacy opened a satellite at Appomattox in 2012, with Lee’s sword as its centerpiece, Rawls came under attack for flying the flags of individual Confederate states, but not the divisive square Southern Cross pattern, carried into battle by Lee’s Army of Northern Virginia, or the elongated rectangular Naval Jack pattern used by the Army of Tennessee — both symbols of racism or Southern pride, depending on one’s point of view.

"They hide behind the first national flag," said Jennings, referring to the so-called Stars and Bars, adopted in March 1861 by the Confederate government, and loosely patterned on the Stars and Stripes. "They’re just scared of the battle flag."

Visitors to the museum in downtown Richmond are greeted at the entrance by a stylized version of a different flag, one that flew at Lee’s headquarters. But in the hushed galleries of the second floor, eight fraying Southern Cross battle flags, captured at Gettysburg 152 years ago, hang in custom-made conservation frames.

"When people see this flag, this is what they think of as the Confederate flag," said the exhibit’s curator, Cathy Wright. "But we wanted to explain that there are really a plethora of patterns and designs."

To that end, the next gallery over features a flag fashioned from a fringed burgundy shawl. On display there, as well, are samples of what Coski, the historian, calls "endless kitsch" — a comic book showing a black woman wearing a Confederate flag uniform, a pair of flag shorts, a photograph of RuPaul, the drag queen, in a long sequined flag gown.

In his 2006 book, "The Confederate Battle Flag: America’s Most Embattled Emblem," Coski traces the evolution of the flag and its different meanings to different people. With political support for flying the battle flag eroding in the wake of the massacre of black churchgoers in South Carolina, he and the book have been in hot demand. The museum bookstore was sold out last week, and at one point, Amazon.com listed it as "temporarily out of stock."

The soft-spoken scholar says he is "conscious that a horrible tragedy is the occasion" for his life’s work to be "picked up and discovered," and he finds that "very sobering." As for the searing debate over the flag, he sees this as "a huge watershed," but one of many, and he does not expect it to go away anytime soon.