When 25 leaders of the largest organization of US nuns met for the first time with Archbishop J. Peter Sartain of Seattle in 2012, after the Vatican appointed him to lead an overhaul of their group, they expected conflict.

The nuns were hurt and confused when the Vatican accused them a few months earlier of straying from Catholic teaching and promoting “radical feminist themes incompatible with the Catholic faith.” And for many Catholics, the appointment of Sartain and two other bishops amounted to a hostile takeover.

“Things were still quite raw,” said Sister Carol Zinn, the past president of the Leadership Conference of Women Religious, which represents about 80 percent of American nuns. “Our board members were saying to him, ‘What do we say to them, Archbishop, what do we say to our sisters?’”

But instead of lecturing the nuns — women who had dedicated their lives to teaching, health care, academia, and social justice — Sartain listened.

“That continued for the next two years,” Zinn said, and it helped lead to a breakthrough: Last month, the leaders of the group say, they were stunned to find themselves at a cordial meeting in the Vatican with a smiling Pope Francis, talking with him for nearly an hour about religious life and their calling to care for the poor and suffering.

The nuns’ journey from pariah status to a papal welcome and photo opportunity lasted three years and was conducted behind closed doors. Despite an outpouring of support by Catholics in support of the sisters and intense interest from the news media, the nuns’ leaders agreed with their bishop overseers from the beginning that they would not talk to reporters about their negotiations.

Even after the process wrapped up abruptly last month with a final joint report, the nuns and the bishops agreed to a 30-day media blackout. But with that interval now over, three leaders of the nuns group and one of the bishops recounted in interviews the sometimes painful route to reconciliation.

The bishops spent many hours listening to the sisters, the nuns said, absorbing their acute sense of betrayal at the accusation that they had been disloyal to the Church to which they had devoted their lives. The sisters reassured the bishops that some of the provocative speakers whom the Leadership Conference had hosted at their conventions did not speak for the whole organization.

“We have learned a lot about the power and the potential of respectful and honest dialogue,” said Sister Sharon Holland, the current president of the Leadership Conference, in a joint telephone interview last week with two other leaders.

No files were ransacked, no staff members dismissed and no major changes were made to the operations of the Leadership Conference, those interviewed agreed. They reached a resolution two years ahead of schedule, short of the five years the Vatican gave the bishops.

An investigation initiated under Pope Benedict XVI came to an early end under Francis, but those involved hesitated to make papal comparisons. They said the process went surprisingly smoothly because they shared a devotion to the Church and realized that the Vatican’s heavy hand with the nuns had caused an uproar among Catholics and damaged the Church’s image.

“My impression was that everybody involved, from the pope to the congregation officials in the Vatican to the bishops and the nuns, wanted to see this get resolved as quickly as possible,” said Bishop Thomas J. Paprocki, one of the three bishops involved. “We were treating one another as fellow Christians, and nobody liked the idea that the outside world saw us as adversaries.”

The adversarial tone was set by the initial “doctrinal assessment” of the Leadership Conference, published in April 2012 by the Vatican’s Congregation for the Doctrine of the Faith, often called the CDF.

The assessment accused the conference of questioning Church teaching on the male-only priesthood and homosexuality, and of allowing speakers at annual assemblies whose addresses contained “serious theological, even doctrinal errors.”

It detected “certain radical feminist themes incompatible with the Catholic faith” in the Leadership Conference’s programs, and it said the group was an ardent promoter of social justice but was “silent” on abortion and euthanasia. What apparently set off alarms in the Vatican’s doctrinal office was a talk by a sister who spoke of “moving beyond the Church” and even beyond Jesus — which the Vatican’s assessment said was “a serious source of scandal.”

But the nuns’ leaders detected a ray of hope in their very first meeting, in Rome, with Sartain. The sisters say he told them, “We’re going to be working together.”

“He did not come to us with a process in mind and he was not given one by the CDF,” said Zinn, the past president of the Leadership Conference. “The only criteria for him was we would build a relationship and have conversations that were mutually respectful.”

Sartain declined requests for an interview. A spokesman, Greg Magnoni, said, “He just has preferred to communicate directly with the sisters throughout.”

At the Leadership Conference’s assembly in August of 2012, after the Vatican’s assessment had been issued, hundreds of nuns sitting at round tables in a hotel in St. Louis debated and prayed over what course of action to take. Some had publicly proposed noncooperation. Others proposed becoming an independent entity from the Vatican.

Instead, they decided to instruct their leaders to “preserve the integrity of the Leadership Conference, but enter the dialogue,” said Holland, who attended but was not yet president.

“It took a lot of courage,” said Sister Marcia Allen, now the president-elect of the Leadership Conference, “to have enduring and patient conversation with the CDF and its representatives.”

The sisters said Sartain asked the nuns to provide him with readings and documents about the Vatican’s instructions to the sisters after the Second Vatican Council, which called for religious orders to modernize their mission and purpose and engage more with the world. He wanted to better understand that history since he was not a member of a religious order.

The conversations focused on doctrine, said Paprocki: “The perception had been given that the sisters were abandoning their Christian identity, and they assured us that wasn’t true.”

After about a year and a half of patient listening (“And it did require patience,” Paprocki said), the bishops and nuns formed a subcommittee to rewrite the Leadership Conference’s statutes. It helped greatly, he said, that the subcommittee included Holland, a canon lawyer who had worked many years in the Vatican. The bishops intentionally enlisted a female canon lawyer as well, said Paprocki, “so it wouldn’t just be the sisters talking to a group of men.”

The rewritten statutes, about 10 pages long, clarify that the Leadership Conference is “an official entity established by the Holy See under canon law,” he said, “centered in Jesus Christ and the teachings of the Church.” But the group is no less independent or in charge of its own affairs than before the process began, he said. The Vatican approved the new statutes.

“Could this have been done better in a less painful way?” said Paprocki when asked whether he thought the whole episode was necessary. “Perhaps. We’re all human.”

Zinn said that she has no idea whether Francis ever directly intervened, but that when called to his office, the pope — a member of the Jesuit order — greeted them as a brother to his sisters.

“That was the surprise of it all for me. It was a conversation,” said Allen. “It was a back and forth of concerns and ideas. I was prepared for him to speak to us. But he was interested in what we were thinking.”