Correction: An earlier version of the article incorrectly defined the term “tailhook.” It is the hook on an airplane that catches a cable while landing on an aircraft carrier, not the cable itself. This version has been corrected.

For more than two decades, the Navy has labored to overcome and bury memories of perhaps the worst scandal in its history: the 1991 Tailhook convention, when crowds of drunken aviators sexually battered scores of women during a frenzied Las Vegas party.

As a result, the Navy brass is reeling over this week’s disclosure that one of its most prominent pilots is under investigation for allegedly fostering a culture of sexual harassment, hazing and lewd behavior.

The pilot, Capt. Gregory McWherter, is the former commander and public face of the Blue Angels, the Navy’s elite flight squadron. Less well known is the fact that until Friday, he also was president of the Tailhook Association, a nonprofit aviator fraternity that despite its past disgrace still draws thousands to its annual convention.

McWherter was relieved of duty as executive officer at Naval Base Coronado, near San Diego, on April 18, three weeks after Navy investigators received a complaint from a former member of the Blue Angels who accused him of tolerating and encouraging sexual misconduct. The Blue Angels perform thrilling maneuverers at air shows and have iconic status in the Navy.

In general, Navy aviators have tried to soften their reputation as a club of hard-drinking, chest-thumping daredevils with outdated attitudes toward women. The Tailhook conventions are more subdued these days. The gathering is held in Reno, Nev., instead of Las Vegas, and is now officially called a symposium.

The 1991 scandal, however, is still considered a dark stain on the Navy’s collective character. More than 140 pilots were investigated for assaulting at least 83 women, forcing many of them to run a gantlet in a hotel corridor. The term Tailhook — the name for the hook on an airplane that catches a cable while landing on an aircraft carrier — became synonymous with debauchery.

With that history, some officers worry about the Tailhook Association’s future if the Navy investigation finds proof that its president condoned sexual harassment or the mistreatment of women.

McWherter did not respond to e-mails seeking comment. On Friday, however, he submitted his resignation as president of the Tailhook Association, saying he didn’t want the inquiry to be a distraction, said Evan M. Chanik, a retired Navy vice admiral who serves as the group’s chairman.

“He didn’t want these distractions to inadvertently affect the Tailhook Association in any way, shape or form,” Chanik said. “I think that’s a mark of his character.”

The harassment investigation comes at a sensitive time for the military. Commanders are struggling to cope with what they describe as an epidemic of sex crimes in the ranks. Some lawmakers are pushing for an overhaul of the military justice system.

Chanik acknowledged that public perceptions about Tailhook and Navy aviators have been hard to shake. “Unfortunately there is that connection from 23 years ago, and people will do with that what they will,” he said. “But a lot of things have changed in the military and society since then.”

McWherter, whose pilot call sign is “Stiffy,” is a former instructor at the Navy’s Top Gun fighter weapons school and a graduate of the Citadel. He commanded the Blue Angels during two stints between 2008 and 2012.

Last month, a former member of the flight squadron filed a complaint with the Navy’s inspector general. It alleged that he tolerated sexual harassment and promoted a work atmosphere rife with hazing, pornographic displays and jokes about sexual orientation.

The Navy is still investigating, but Navy officials decided that the preliminary findings warranted McWherter’s removal from his job at Coronado.

Supporters are angry about his removal and have started a Facebook page filled with testimonials about his integrity.

“We want the Navy to know we support this man,” said Sherri Viniard, a friend from Covington, Ga., who set up the page. “Lots of people who know him and have worked with him know these allegations just can’t be true.”

Lt. Cmdr. Amy Tomlinson, the only female aviator to fly with the Blue Angels, served under McWherter from 2008 until 2010. She called him a “very, very good” commander and role model.

“I loved being a Blue Angel and I loved working with him,” said Tomlinson, who is now in the Navy Reserve. “I still hold him in very high regard, no matter what anybody says. He’s an outstanding leader in every way.”

Other women have been assigned to the team as support officers and in enlisted jobs.

Some veterans have grumbled that the world of Navy aviation has become too tame and emasculated in an overreaction to the 1991 Tailhook convention and other modern pressures to sanitize the workplace.

Former Navy secretary John Lehman has called the Tailhook investigations “a grotesquely disproportionate witch hunt” that caused pilots to become risk-averse and too worried about political correctness.

“Suspicions of sexual harassment, homophobia, telling of risque jokes, and speech likely to offend favored groups all find their way into fitness reports,” he wrote in a 2011 article for the Naval journal Proceedings. “And if actual hot-line investigations are then launched, that is usually the end of a career, regardless of the outcome.”

But Paula Coughlin, a retired Navy officer who was assaulted at the 1991 Tailhook convention, questioned whether the old culture and habits have changed much. When she was in the Navy, she recalled, the Blue Angels were particularly well known for masculine excesses.

“They came across as the most clean-cut family guys you ever saw, just perfect poster boys for military recruiting,” she said. “But when it came down to it, they were just a bunch of pigs. After the show was over and the lights went down, these were the guys totally on the prowl, always looking for a hookup.”

Julie Tate contributed to this report.