After a stormy year in which longtime New York City Ballet director Peter Martins resigned amid scandal, followed by a lawsuit alleging sexual harassment that led to the departures of three top male dancers, the company has announced new leadership. Jonathan Stafford, 38, a former dancer and part of the interim leadership team, has been appointed artistic director of the company and its training arm, the School of American Ballet.

Former NYCB star Wendy Whelan, 51, who retired in 2014 after a 30-year career, will be associate artistic director, starting March 12. Resident choreographer Justin Peck gets an additional title: artistic adviser.

Stafford and Whelan broke the news to the dancers in a packed meeting Thursday morning. “You could hear a pin drop in the studio,” said principal dancer Teresa Reichlen. Applause followed the silence, said Reichlen, who was nearly moved to tears.

Whelan breaks a thick glass ceiling at the internationally esteemed NYCB, which, since its inception, has been led exclusively by men: founder George Balanchine, followed by Martins in partnership with choreographer Jerome Robbins, and then Martins alone. In a career of extraordinary distinction, Whelan mastered more than 50 ballets and was a favorite with audiences and such leading choreographers as Robbins, Alexei Ratmansky, Christopher Wheeldon, Twyla Tharp and William Forsythe. Since retiring, Whelan has pursued a solo career, also to great acclaim. She applied for the NYCB directorship, and a petition to hire her collected nearly 16,000 signatures.

Speaking by phone Thursday, Stafford and Whelan said that Stafford will handle the day-to-day artistic operations of the school and the company. Whelan will oversee programming, commissioning new works, coaching dancers in rehearsals and teaching.

“I feel extremely good about where I’ve landed,” Whelan said. “I hope to learn from Jon and continue with what I do well, which is artistic collaborations and reaching outside the company for commissions.” 

Whelan said the dancers’ response to their announcement reminded her of when Martins took over the company, a transition she witnessed as a young dancer.

“Anytime there’s a change, there’s a lot of confusion and questions,” she said. “That’s the natural way for things to go. This will be the same. It will take a lot of work. . . . We’re trying to remove all this negative, bad energy and bad thinking.”

Negative press has been the norm at the company for more than a year, with headlines such as the New York Post’s “It’s ‘Swine Lake’ at the NYC Ballet/#MeTutu I was sexually exploited by abusive ‘frat boy’ dancers.” Former SAB student Alexandra Waterbury has sued the company and dancer Chase Finlay, alleging the sharing of sexually explicit images of unknowing female dancers. Finlay resigned and dancers Amar Ramasar and Zachary Catazaro were fired.

“For many years,” Waterbury’s complaint alleges, NYCB has “encouraged and permitted its male dancers to abuse, assault, degrade, demean, dehumanize and mistreat its female dancers and other women.” 

In January 2018, Martins stepped down amid accusations of violence and sexual harassment, which he denied but that several of his dancers described to The Washington Post and the New York Times.

NYCB and its school came under more criticism for the way they handled the complaints — by jointly commissioning an investigation that did not corroborate the allegations yet which prompted the company to draw up policies to better protect the dancers. The turmoil this past year has raised concerns among ballet insiders and other observers about an enabling culture at NYCB that has left dancers and students at SAB vulnerable to abuses inside and outside the studio.

“I can speak emphatically that there’s not an unhealthy climate here,” Stafford said. New measures he has instituted include annual performance reviews, which allow dancers to voice their concerns. He’s also invited in former Balanchine stars to coach the dancers, including Patricia McBride, Edward Villella and Mikhail Baryshnikov. But Stafford had no definitive word on whether Martins would be among those coaches when his ballets were being rehearsed.

“Peter Martins’s involvement will be under consideration,” he said. “This is a really great moment in time when Wendy and I can look at everything.”

Reichlen said the appointments felt like “a step in the right direction.”

“First of all, acknowledging that the job was larger than one person could handle was great for the boards of both the school and the company to decide,” she said.

“Wendy’s always been my idol growing up, so for me to continue to work with this amazing woman — it gave me a lot of hope for the direction of the company,” Reichlen added. “They’re making a huge statement by hiring a woman, and her breadth of knowledge and experience, and the number of choreographers she’s worked with is so vital for the specific mission of our company.”

Whelan said she will continue with plans to perform “The Day,” an hour-long solo choreographed by renowned modernist Lucinda Childs, accompanied by cellist Maya Beiser. She’ll dance it in July at Jacobs Pillow Dance Festival, with plans for New York’s Joyce Theater, the Kennedy Center and also Paris, in 2020. But she said she doesn’t have plans beyond that.

Whelan’s 2016 documentary about her last year as a ballerina, “Restless Creature,” captured acute tensions between her and Martins; he took her out of “The Nutcracker,” for example, leaving her distraught. But she said her new post was not a vindication.

“This feels like my opportunity to make the changes that I needed, to understand the dancers at a new level than what I left with,” she said. “When I left I was confused, really coming out of a skin of the company that was what I grew up in.”

With a few years’ distance, Whelan said, she has gained an understanding of herself and her past, and this is what she wants to bring to the dancers “in a human way.”

“I want to offer them what I felt was lacking: communication. I want to get that communication right, and get it kind and caring.”