The rainbow flag flies beneath the American flag at the Stonewall National Monument on Oct. 11 in New York. (Mark Lennihan/AP)

The plan to celebrate the rainbow flag flying over Stonewall National Monument was going smoothly. Then things got weird.

Activists had pressed for months to get the flag — a long-standing symbol of the lesbian, gay, bisexual and transgender community — hoisted atop the flagpole adjacent to the national monument that President Barack Obama designated last year to commemorate the LGBT civil rights movement. The National Park Service agreed to do it, providing a flag that went up Sept. 28, and it worked with activists to put on an event commemorating the act on Wednesday, which was also National Coming Out Day. NPS officials provided the federal permit free of charge, as well as power and a sound system for the rally, and the monument’s chief interpreter initially agreed to speak.

On Thursday, however, Newsweek ran a story calling the rainbow flag flying on federal land “a rainbow-colored triumph whose meaning is compounded by the shadow President Donald Trump’s administration has cast over LBGT rights.” One of the event’s organizers, Ken Kidd, criticized the Trump administration for rolling back several Obama-era protections for LGBT people, saying that when one examines the men and women Trump has chosen for his Cabinet, the “one thing they all consistently have in common is an anti-LGBT agenda.”

By Friday evening, according to Kidd, the NPS flag that had been flying alongside the rainbow flag was taken down “under the cover of darkness,” and a New York City Parks flag was raised in its place. The agency official who had offered to speak at the celebration, Barbara Applebaum, canceled, citing a scheduling conflict.

“Our contact with the National Park Service became strained,” Kidd said. “I got a call Saturday afternoon, while I was apple-picking.”

Joshua Laird, commissioner of the National Parks of New York Harbor, said in an interview Wednesday that Interior Department officials had made “an inquiry” late last week to his office to determine whether the rainbow flag would be the first one to fly on the grounds of a national monument. But NPS officials determined that the flagpole was on city property, rather than the 7.7-acre patch of land in Christopher Park that constitutes the monument itself.

“We did send mixed signals here, which was very unfortunate,” Laird said. “It became a much bigger deal than we ever expected.”

The monument — which ranks as the first national monument dedicated to gay rights — drew protests from conservatives when it was declared but ranked as a high priority for top Obama administration and New York federal, state and local officials.

After police raided Stonewall Inn, which was frequented by gay men, in 1969, a six-day-long series of protests began at the site in the early morning of June 28. The uprising helped galvanize the modern LGBT movement.

Laird emphasized that the rainbow flag was never removed and that the National Park Service has donated it to the city. He said that Interior Department officials in Washington did want to know whether “it was accurate” that the rainbow flag would set a precedent by flying on federal property but that he would not describe administration officials as raising “a concern” about it. The Department of Interior did not respond to a request for comment.

“It’s still up, it’s still flying there,” Laird said of the flag. “Visitors to Stonewall National Monument will see it, and 99 percent of them will not care if it’s on our property or [the city’s] property.”

Shortly before the ceremony, Laird offered to speak at the celebration, and Applebaum changed her schedule to attend the event. But the men and women who had lobbied to hoist the flag refused the offer.

“We said, no, you will not speak,” said Ann Northrop, host of the public access show “Gay USA” and the event’s emcee. “This is completely just mean-spirited bigotry on their part, to find a technicality to pull out of what they had already agreed upon and worked on for a week.”

The ceremony went ahead, with the playing of the national anthem (some in the crowd of about 100 took a knee) and the singing of “Somewhere Over the Rainbow.” It lasted about 45 minutes.

“That flag is flying proudly over the Stonewall National Monument in New York City,” Kidd said. “That symbol is up there for all the people who need it — and boy, do we need it more than ever.”