Salwan Momika, an Iraqi immigrant who set off enormous protests when he burned a Quran in Stockholm in 2023, has been killed, the Swedish Prosecution Authority said Thursday morning.

The police said that they had arrested five people and that a murder investigation had been launched. Mr. Momika had been set to appear in Stockholm District Court on Thursday on charges related to the 2023 incident, which resulted in protests in Sweden and across the Muslim world.

The Stockholm police, who declined to confirm that Mr. Momika had been killed, said that there had been a shooting late on Wednesday in Sodertalje, a city near Stockholm, and that a man had died. The prosecution authority then confirmed that Mr. Momika was that man.

Mr. Momika’s defense attorney, Anna Roth, said he had received death threats. The authorities did not say if they believed the killing was connected to Mr. Momika’s burning of the Quran.

Mr. Momika, a Christian, had set the Quran ablaze during Eid al-Adha, a major Islamic holiday, outside a mosque in Stockholm. He said that he was trying to raise awareness about the mistreatment and killing of Christian minorities by Islamists in some parts of the Muslim world.

“I am warning the Swedish people about the dangers of this book,” Mr. Momika had said through a megaphone outside the mosque.

The response from the Muslim world was swift and furious, with much of the criticism aimed at the Swedish authorities for not stopping the burning.

In Iraq, several hundred people stormed the Swedish Embassy in Baghdad and set parts of it ablaze. Iraq expelled Sweden’s ambassador and directed its ambassador to Sweden to withdraw from its embassy in Stockholm.

Egypt called the Quran burning “a disgraceful act.” And Morocco recalled its ambassador in Sweden, its state news agency reported.

The Swedish authorities had condemned Mr. Momika’s actions at the time, but the police granted a permit for his planned demonstration after a Swedish court ruled that banning it would impinge on the right to freedom of speech.

The permit, however, did not allow him to burn objects, and Mr. Momika was subsequently charged with agitation against an ethnic or national group in four incidents of kicking, stamping on and burning a Quran. He also made speeches with derogatory statements directed against Muslims and Islam, according to the indictment.

“The fact that statements are made in a large square and disseminated is a prerequisite for incitement to racial hatred,” said Anna Hankkio, a Swedish prosecutor who initially brought the charges against Mr. Momika. “It is up to the district court to assess whether the burning of the Quran can also be considered incitement against a group of people.”

Later that summer, Mr. Momika again burned Qurans, according to the indictment.

The Quran burnings — and the resulting horror and outrage from the Muslim world — sparked debates in Sweden, which has struggled with whether to allow such protests.

Before Mr. Momika burned the holy book, Swedish authorities had denied other anti-Quran protests, citing concerns about disruption to public order. After the burning, Sweden’s foreign ministry called Mr. Momika’s action Islamophobic, and officials warned that such protests could affect the country’s national security policy. The domestic security agency briefly raised its terrorism threat to its most severe designation.

Salwan Najem, who joined Mr. Momika in some protests and was also accused of burning a Quran, was a co-defendant in the case that was to be decided on Thursday. He is now set to receive his verdict on Feb. 3, the Stockholm District Court said in a statement.

On Thursday, Mr. Najem expressed fear, posting a link on X to a story about Mr. Momika’s killing.

“I am next,” he wrote.

As he does every three months, Sibusiso traveled on Wednesday morning to a clinic in the capital of Eswatini, a tiny southern African nation, to get a refill of the H.I.V. medication he needs to save his life. When he arrived, the door was locked and about 20 other patients stood outside, baffled that the clinic was closed.

Sibusiso, 39 and unemployed, had heard rumors that President Trump was pulling funding for the program that supported his treatment. Now, though, he learned the reality: The Trump administration had ordered a halt to the President’s Emergency Plan for AIDS Relief, or PEPFAR, one of America’s most consequential aid programs in Africa.

The abrupt pause of a $6.5 billion program established by former President George W. Bush and credited with saving the lives of tens of millions of people sent patients, clinicians and public health advocates across Africa into a panic. Many feared a return to some of the darkest days on the continent, when H.I.V. spread rapidly and a diagnosis was akin to a death sentence.

As Sibusiso stood outside the clinic, he feared he could be next. He had taken the last of his antiretroviral medication that morning. And even though the Trump administration had backtracked, suddenly announcing on Tuesday that lifesaving medications and treatments could continue to be distributed, the clinic remained shuttered in the confusion.

Sibusiso, standing outside, had no idea where or when he could get more medicine.

“I’m now thinking of dying,” said Sibusiso, who requested that only his first name be used to protect his privacy. “What am I going to do without this treatment?”

The Trump administration has said that foreign assistance programs will be paused for three months as it reviews how money is being spent. If the administration decides to end PEPFAR, it could lead to 600,000 deaths over the next decade in South Africa alone, where the program has its largest number of beneficiaries, according to a study.

“The next 90 days are looking so dystopian,” said Nozizwe Ntsesang, the chief executive of a leading gay rights advocacy group in Botswana.

Across South Africa and other countries in the region, fear and uncertainty are palpable. Some African leaders had shared optimism and excitement about a second Trump term. But now, one of his first moves appeared to put lives at risk.

“I’m scared,” said a 19-year-old South African college student who was born with H.I.V. “People will die. It’s going back to the ’90s where people did not have enough medication to treat the disease.”

The student, who also requested anonymity to protect her privacy, said the clinic that she goes to in Johannesburg gave her a three-month supply of her antiretroviral medication on Wednesday instead of the usual six months. Officials explained that they wanted to reserve some stock in case other clinics ran short, she said.

PEPFAR does not provide medication for the South African health system, but it does employ around 13,000 medical professionals, from doctors to community health workers, who are responsible for ensuring that people are tested and seek proper treatment. Virtually all of those employees were ordered to stop working after the Trump administration froze foreign aid programs, according to health care advocates.

The staff shortages, health workers and rights groups said, led to much larger crowds at public clinics in South Africa, where roughly eight million people are living with H.I.V. and 5.7 million receive treatment.

Amid the chaos of the freeze and the Trump administration’s backpedaling, many clinics remained shuttered on Wednesday, with medical workers unsure about the new rules and patients frantic to secure their medication.

Some patients have been forced to wait 10 hours for treatment, advocates said. There were also fears that, without counselors to talk to, some patients, especially those newly diagnosed with H.I.V., would not administer their treatments properly or seek help in the future.

“The abrupt stop is not responsible,” said Solange Baptiste, the executive director of the International Treatment Preparedness Coalition, an organization that works to improve access to treatment for people with H.I.V. “Lives are at risk when you do that.”

South Africa is in a better position than many other African countries. The government procures most of its H.I.V. drugs directly and relies on PEPFAR for only about 17 percent of its overall H.I.V. treatment budget.

Neighboring Botswana, which has received nearly $72 million in aid from PEPFAR since 2003, also buys its own treatment medication, but the work and funding stoppage has weighed heavily on local organizations.

Stanley Monageng said he cried when he learned about the Trump administration’s order. Mr. Monageng, 78, has been running an organization in Molepolole, in southern Botswana, since 2005. It provides support for children with H.I.V. and relies mostly on PEPFAR funding, he said.

Mr. Monageng said he was worried all week that he would not be allowed to provide antiretroviral medication to the dozens of children, many of them orphaned, who rely on his organization for help. Mr. Monageng himself has been living with H.I.V. for 25 years and says he has personally benefited from the PEPFAR program.

“I asked myself, ‘How are these orphans going to survive? How am I going to help them?’” he said on Wednesday from the three-bedroom house that he uses for the center. “I’ve been surviving all these years because of America.”

At HealthPlus 4 Men, the clinic that was closed in Eswatini on Wednesday, officials encouraged anxious patients to go to a public hospital to seek medication. But most patients were uncomfortable with that option.

HealthPlus primarily treats gay men, a population that has been historically stigmatized in Eswatini. Many of its patients fear going to government-run facilities, where they worry they will face discrimination. Public hospitals also often provide prescriptions that many patients can’t afford to fill, said Sibusiso Maziya, the executive director of HealthPlus.

“It’s a sad moment for us,” Mr. Maziya said. “They want to know when this situation will change, when are we opening.”

Despite the waiver issued by the U.S. government on Tuesday, Mr. Maziya said his organization was continuing to withhold antiretroviral medication supplied with PEPFAR funds as it awaits clarity from its funders on what it is allowed to do.

Msizi Mkhabela, the operations manager for HealthPlus, added that the organization promotes diversity, equity and inclusion by supporting equal treatment for gay men. That mission could run afoul of the Trump administration’s freeze on such programs and may put the clinic at a higher risk of being permanently defunded.

In addition to medication, HealthPlus also has a mobile clinic and outreach programs to make sure that people living in rural areas are being tested and receive treatment for H.I.V. The organization considers those programs an essential part of its efforts to prevent the spread of the disease. But all of that was put on hold because the funding came from PEPFAR and HealthPlus is unsure what activities are allowed to continue.

“We are literally shaking and worried,” Mr. Mkhabela said. “Very much frustrated.”

Reporting was contributed by Yvonne Mooka from Molepolole, Botswana, Lynsey Chutel from London and Golden Matonga from Blantyre, Malawi.