I MET SHINTA RATRI 10 days after her life’s work had unraveled before her eyes. She quietly introduced herself as she fumbled to light a cigarette. The mood was different from six years earlier, when dozens of reporters had flocked to Indonesia, home to more Muslims than any other country, to profile Shinta’s unique creation — the world’s only Islamic school run by and for transgender women. In early March, we sat on a terrace to discuss how militant Islamists had forced her to shut down her beloved Al-Fatah Pesantren as an unprecedented anti-LGBT campaign across the country reached fever pitch.

Ibu Shinta, as she is called — “Ibu” is the Indonesian honorific equivalent of “Ma’am” — opened the Islamic boarding school in 2008 in Yogyakarta, a bohemian university city on Indonesia’s Java Island. Now 54 years old, Shinta has lived as a waria, or transgender woman, since she was 18 and, over time, came to know a network of other waria in the city.

Shinta expressed being waria and Muslim by wearing a headscarf and praying daily. Her family and neighbors respected this — and her life was peaceful. But the same wasn’t true for other waria. Many were shunned by their families. Parents often invoked religion when throwing their children out of the house, and isolating the waria spiritually as well as materially. Even waria who could earn a living begging and doing sex work struggled to remain devout. They were harassed at mainstream mosques and turned away. Al-Fatah changed all of that — and more.

“It was a place to pray together, to learn about Islam together,” Shinta told me, leaving her cigarette to ash in a plastic saucer. “Waria were uncomfortable praying in public mosques, so I thought it would be better for us to be together than sitting alone in our homes with our spiritual questions only in our hearts.”

The lessons offered at Al-Fatah were modest. Waria who left home at an early age had their education in Muslim ritual interrupted. Some wanted to learn to read the Qur’an, but many were illiterate. Shinta and others taught about sacramental cleaning before daily prayers, and how to memorize verses of scripture. On Sunday evenings, a group of up to 40 would convene to pray together, then ask how they should interpret their life’s problems according to Islam.

One common question was about the ethics of sex work. “Waria would come and ask me if doing sex work was haram (forbidden by Islam),” Shinta said. “It was a very stressful question for them — they didn’t have any other way to earn money.” Shinta offered an explanation that pacified their fears and solidified their faith: if the sex work transaction is an honest one, and they do not use the money they earn to harm people but to live a good life, then their actions are acceptable in the eyes of God.

Al-Fatah attracted support from local religious leaders. Professors from Islamic universities would visit Shinta regularly, she said, and express their gratitude for her offering Muslim spiritual guidance to the waria community. Indonesia’s most influential Muslim organization, the 50 million–member Nahdlatul Ulama, quietly supported Shinta’s work, she said.

For Shinta, the positive feedback had both practical and spiritual dividends. “Over time, waria — especially those who did sex work — became more comfortable speaking up, and more comfortable with themselves because we reestablished what it meant to have a family for them,” Shinta said. Lighting another cigarette as the first got soggy with the spring humidity, she recounted how during the 2015 Eid al-Adha, a very important four-day annual holiday, Al-Fatah had no money to purchase an animal for the ritual slaughter and feast. Instead, the waria gathered to read the Qur’an together. “Only 10 of us were able to read it at all,” Shinta said, “so we divided the book into three sections to read and the others sat and listened.”

Three days into the group reading sessions, a neighbor stopped in with a wad of cash to donate. “It was enough to buy a goat and celebrate Eid like everyone else,” Shinta said. “And for the waria community, it showed that Allah had heard our prayers.”

But Al-Fatah — a modest building tucked behind a mosque on Shinta’s family land — was more to Yogyakarta and to Indonesia than a house of worship for devout transgender women. It was also a potent symbol of pluralism at a time when militant intolerance was sweeping the country — often at the expense of minorities.

Historically, many Indonesian sexual and gender minorities have lived with a mix of tolerance and prejudice. Discretion purchased safety: many lesbian, gay, bisexual, and transgender people chose to live without publicly disclosing their sexual orientation or gender identity, in order to protect themselves from discrimination or violence. Waria were particularly visible — but even in the Sharia-ruled Aceh province, they operated hair salons. Some regions of the country celebrated gender diversity more than others — the island of Sulawesi was home to cultures that recognize five gender categories, for example. But in January 2016, seemingly out of nowhere, government officials, militant Islamists, and mass religious groups stoked unprecedented anti-LGBT intolerance.

The onslaught began on January 24, when the higher education minister, Muhammad Nasir, said he wanted to ban LGBT student organizations from university campuses, saying that such groups were not “in accordance with the values and morals of Indonesia.” Within weeks, statements ranging from the absurd to the apocalyptic echoed through Indonesia’s media. At a maternal health seminar, a mayor warned young mothers off instant noodles — their time and attention, he said, should be given instead to nutritious cooking and teaching their children not to be gay. The defense minister labeled LGBT rights activism a proxy war on the nation led by outsiders, more dangerous than a nuclear bomb.

The cacophony of public condemnation quickly grew into calls for criminalization and “cures” — and opportunistic attacks on public figures such as Shinta.

Mainstream mass religious groups, including the traditionally tolerant Nahdlatul Ulama, called for criminalization of homosexuality and LGBT rights activism, and for forced “rehabilitation” of LGBT people. The Indonesian Psychiatric Association joined the anti-LGBT chorus by proclaiming same-sex sexual orientation and transgender identities “mental illnesses” and recommending psychological rehabilitation. On February 23, police violently cracked down on a peaceful LGBT solidarity demonstration in Yogyakarta. Some kilometers away, a militant Islamist group held a counterdemonstration, threatening to murder LGBT people as sinners against Islamic principles.

On February 24, another militant Islamic group, the Islamic Jihad Front (FJI), went to Al-Fatah and demanded it be shut down. Shinta, with the help of legal aid lawyers, tried to get the police to protect the school, but their reaction was influenced more by fear of the Islamists than the rule of law. “The police told me I should have a discussion with the fundamentalists,” Shinta said. “The police scolded me: ‘we are Javanese, we welcome our guests openly — these are your guests, so welcome them.’”

Two nights later, the FJI summoned Shinta to the community meeting hall. She arrived on time, and was greeted by her friends and neighbors warmly. “As I walked in, people greeted me Muslim-to-Muslim, neighbor-to-neighbor, as they have my entire life,” Shinta recounted. Then five minutes later when the FJI representatives arrived, heralding their entrance with shouts of “Allahu Akbar,” the tone in the room changed dramatically.

The militants listed bureaucratic reasons why Al-Fatah should be shuttered. Among them: The waria park their motorcycles in the street, causing traffic jams and inconvenience — a complaint Shinta had never received. Then they asked Shinta to speak — to explain herself as a waria.

“I told them about how Islam accommodates diversity — people with disabilities, waria, all kinds of people deserve Allah’s love,” Shinta explained. “I recited passages of the Qur’an, and explained how we teach waria how to face death as Muslims, how to pray as Muslims. I told them about how I was a boy when I was born, but my soul is that of a woman.”

When Shinta concluded, the room was left in a tense calm. Most people there had known her their whole lives, and Al-Fatah had been a part of the community for nearly a decade now. They were also keenly aware — as all Indonesians are — of the power of militant Islamist groups.

“Shinta is very smart,” an FJI leader stood and said. “She is also mentally ill. We know there are men and women and nothing in between — so she is sick, and what she is teaching here is harmful to Islam. It must be brought to an end.”

There was no vote, and only FJI issued a formal announcement — not the local government, not Al-Fatah. But even as Shinta left the meeting hall that night, she could sense the shift that had occurred. Stoked by fear, the pluralism she had cultivated through her pious endeavor was crumbling. As she left the building holding back tears, she heard one neighbor whisper to another: “So it’s not Ibu Shinta now, it’s Mas (mister) Shinta.”

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Kyle Knight is a researcher in the LGBT rights program at Human Rights Watch.