“The realities so far is that the H.T.S. and also the other armed groups have been sending good messages to the Syrian people,” Mr. Pedersen said, referring to Hayat Tahrir al-Sham, the militant group at the head of the lightning advance that ended half a century of Assad family rule.

Hayat Tahrir al-Sham and other armed groups controlling Damascus, the capital, have issued “reassuring statements” about forming a government of “unity and inclusiveness,” Mr. Pedersen said. But he warned of the dangers of renewed violence among the patchwork of armed groups operating across Syria, citing continuing clashes between groups in the northeast, and of the risks posed by what he called Israel’s “very troubling” military operations in the country.

The Israeli military seized control of a buffer zone between Syria and the Israeli-occupied Golan Heights over the weekend, and in the past two days its forces have carried out strikes on airfields, military warehouses and other targets around Damascus and the port city of Latakia.

“This needs to stop,” Mr. Pedersen said. As Syria’s armed groups attempt an orderly transition to a new government, it is “extremely important that we don’t see any action from any international actor that destroys the possibility for this transformation in Syria to take place,” he added.

Mr. Pedersen urged Syria’s armed groups to protect civilians and to move toward a government based on the broadest possible representation of the country’s many ethnic and religious communities.

“If we do this, if we unite the Syrian parties, we bring together the different Syrian communities, then this could be the real beginning of something new for Syria,” he said.

The United Nations has listed Hayat Tahrir al-Sham as a terrorist group for the last nine years based on its past association with Al Qaeda. Mr. Pedersen said that this was a complicating factor but added that he believed the formation of an inclusive government would lead the international community to reconsider the designation.

“We also have to be honest — we have to look at the facts and to see what has happened during the last nine years,” Mr. Pedersen said, citing the group’s messages of inclusiveness and “reassuring things on the ground” in the areas it controls.

But Sobhi Firwana, 29, said that he was concerned that the situation in Syria could prolong the war in Gaza and further delay efforts to reach a cease-fire, pointing to the media’s pivot of coverage to Syria and Israel’s bombing campaign there.

Even as Israel pummeled targets in Syria, saying it was destroying military and weapons facilities there, its forces have continued strikes in Gaza. On Monday night, 25 people were killed in an airstrike on a house in Beit Hanoun, a town in northern Gaza, according to Mahmoud Basal, a spokesman for the Palestinian Civil Defense emergency service.

The Israeli military, which has called for evacuations of much of north Gaza, did not immediately comment on the strike, but it has been conducting an offensive there to try to extinguish a Hamas resurgence. It maintains that it tries to avoid civilian casualties but that Hamas has embedded itself in residential areas.

The deadly attack “due to the events happening in Syria and the diversion of the media coverage, possibly did not echo,” Mr. Basal said in a statement on Tuesday.

Talks on a cease-fire in Gaza are quietly advancing behind the scenes, according to mediators and officials, but details remain murky and an agreement is not in hand. Mr. Firwana, a lawyer and law professor from Khan Younis, said he was concerned that the situation in Syria could further push back a deal because Israel was now focused on securing its borders from potential threats in Syria.

But Ahmed Khalil, a 29-year-old from central Gaza, said he thought that the fall of Bashar al-Assad, along with the deaths of Hezbollah leaders in Lebanon, sent a strong message to Iran.

Iran has sustained blow after blow at the hands of Israel and the ouster of Mr. al-Assad severely damaged Iran’s regional strategy, which cultivated a network of allies, including Hamas, Hezbollah and the Syrian government.

Mr. Khalil said he thought that Iran’s weakening influence could “hasten the process of negotiations for a cease-fire and a deal for prisoners in Gaza.” If a cease-fire is reached in Gaza, the bakery worker said he would celebrate like many in Syria have over the last week, by preparing and handing out local desserts.

Husam al-Fiqy, a 41-year-old from Nuseirat in central Gaza, said that he was indifferent to the details of what happened in Syria, but he felt a sense of relief seeing the Syrian people “finally free themselves from their oppressive leader.”

He gave no details about how the rebel group would pursue that course, or of any judicial process, which human rights experts say is essential to helping Syria move forward.

The group Mr. al-Shara leads, Hayat Tahrir al-Sham, had earlier announced an amnesty for the rank and file of the government of former president Bashar al-Assad, but Mr. al-Shara said this did not extend to senior officials. His comments came amid fear that people who supported the fallen government could face retribution.

The group confirmed the appointment of Mohammed al-Bashir as the country’s prime minister on Tuesday, according to SANA, Syria’s state-run news agency. Mr. al-Bashir has been tasked with running the transitional government until March 1, the agency reported. He previously served as the head of a rebel-run administration in northwestern Syria.

Hayat Tahrir al-Sham, an Islamist group that was once linked to Al Qaeda, has tried to gain international legitimacy by eschewing global jihadist ambitions and focusing on organized governance in Syria. But it has also come under criticism for using authoritarian tactics and cracking down on dissent.

Human rights groups say that more than half a million people including around 200,000 civilians, died in Syria’s civil war, which began in 2011, but attention has focused on atrocities committed by Mr. al-Assad’s government.

The whereabouts of around 136,000 people who were arrested arbitrarily by the Assad regime is unknown and in many cases the government did not acknowledge that people had been detained, leaving family members in the dark, according to the Syrian Network for Human Rights. In addition, at least 15,000 people were tortured to death by the government, the network said.

Human rights experts say a judicial process is necessary and that the options for the rebel alliance include building cases in national, foreign and international courts. But they caution that it would take time to set up a national system capable of rendering justice and it can only be done once security in the country has been established.

Human rights groups in Syria, working with international organizations, have spent more than a decade documenting evidence of crimes committed in the country, particularly in the regime’s notorious prison network.

In addition, there have been around a dozen prosecutions in courts outside Syria. In one high-profile example, a court in the city of Koblenz, Germany, sentenced a former intelligence officer to life in prison in 2022 after he was convicted of crimes against humanity.

The court found that the former officer, Anwar Raslan, 58, oversaw the torture of prisoners in Damascus and the killing of at least 27 people there, in addition to the sexual abuse and rape of detainees.

The ultimate target for human rights groups working on Syria would be to bring Mr. al-Assad to justice. Russia announced over the weekend that Mr. al-Assad had arrived in Moscow and would be granted asylum, apparently putting him out of reach.

It was unclear what had caused the damage in the photographs, but Israeli officials said that their country was striking weapon stockpiles in Syria, including chemical weapons and long-range missiles and rockets, to prevent Syria’s new leaders from potentially attacking Israel in the future.

Gideon Saar, Israel’s foreign minister, told reporters on Monday that the leaders of Syria’s rebels “are people with an extreme ideology of radical Islam.” Israeli forces are destroying the weapons “in order that they don’t fall in the hands of extremists,” he added.

The Syrian Observatory for Human Rights, an independent group based in Britain that has tracked the civil war in Syria for years, said that it had documented 322 Israeli strikes in Syria since Sunday, when President Bashar al-Assad fled the country. It said the strikes had targeted “warehouses, aircraft squadrons, radars, military signal stations, and numerous weapons and ammunition depots,” including some as recently as Tuesday morning.

The group also said that Israeli forces had pushed further into Syrian territory, past a buffer zone set up by the United Nations.

Avichay Adraee, an Israeli military spokesman, said on social media on Tuesday that Israeli forces “are present inside the buffer zone and at defensive points close to the border in order to protect the Israeli border.” He added that reports that the military was “advancing or approaching Damascus are completely incorrect.”

The region between Israel and Syria has been fought over for decades. Israel captured the Golan Heights during a war in 1967 and annexed most of it in 1981. Most of the world views this area as Israeli-occupied Syrian territory. Beyond the Golan Heights, into Syrian territory, there is a 155-square-mile demilitarized buffer zone that has been patrolled by U.N. troops since the Arab-Israeli war of 1973, also known as the Yom Kippur War.

Israeli ground forces advanced into that zone on Saturday, their first overt entry since 1973. They took control of the summit of Mount Hermon in Syria, a strategic point to oversee the region, as well as other important locations to give them control of the area, Israeli officials said. Prime Minister Benjamin Netanyahu said on Monday that he had ordered the incursion to protect Israeli territory.

“For the time being, we are there,” Mr. Saar said. “But we define these steps as limited and temporary.”

Aaron Boxerman and Gabby Sobelman contributed reporting.

“It’s a wreck now but we want to fix it,” said a fighter with his face covered who gave only his nom de guerre, Abu Oweis. Of the palace, he said: “It is beautiful, but it was all for Bashar.”

He is a fighter with Hayat Tahrir al-Sham, the group that led the rebel charge from Idlib Province in the northwest all the way to Damascus, forcing Mr. al-Assad to flee. Abu Oweis said he was 20, had not finished high school and had never left Syria or visited its largest cities, Aleppo or Damascus.

“It’s a big city,” he said of the Syrian capital. “Really big.”

Outside the presidential palace, a family and their friends were wandering around, marveling at the grandeur of the structure and the landscaped gardens around it.

“I wanted to see all the blood that they drew from us to build this,” said Mohammed Abu al-Kheir, 42, an electronics trader.

“This is really rich, unnaturally rich,” he said, shaking his head. “Just the irrigation needed its own budget.”

In the fallout created by Mr. al-Assad’s downfall, there are big questions about who will step in.

Hayat Tahrir al-Sham

Hayat Tahrir al-Sham, whose name means Organization for the Liberation of the Levant, is a former affiliate of Al Qaeda that broke with the older group years ago and came to dominate the last stronghold of Syria’s opposition.

It was the main rebel group leading the latest offensive, launching a surprise assault in late November out of its base in northwestern Syria that quickly led to the fall of the Assad government.

Members of the group had early links to the Islamic State, and then to Al Qaeda. In 2016, they tried to shed their extremist roots, banding together with several other factions to establish Hayat Tahrir al-Sham. The United States and other Western countries still consider it a terrorist group.

The group’s leader, Abu Mohammad al-Jolani — who as of Monday shed that nom de guerre and is now going by his real name, Ahmed al-Shara — told The New York Times that his primary goal was to “liberate Syria from this oppressive regime.” He has tried to gain legitimacy by providing services to residents in his stronghold of Idlib Province.

Because of its roots and its designation as a terrorist group, Hayat Tahrir al-Sham has struggled to raise funds, according to the Center for Strategic and International Studies, a Washington research institute. The group raises money from border tariffs, collecting taxes on residents and holding a monopoly over utilities. Analysts say it has also been involved in trafficking the synthetic stimulant captagon.

Syrian Democratic Forces

Forces from Syria’s Kurdish ethnic minority, which makes up about 10 percent of the population, became the United States’ main local partner in the fight against the Islamic State in Syria, under the banner of the Syrian Democratic Forces.

After the Islamic State was largely defeated in 2019, the Kurdish-led forces consolidated control over towns in the northeast, expanding an autonomous region they had built there. But Kurdish fighters still had to contend with a longtime enemy, Turkey, which regards them as linked to Kurdish separatist insurgents inside Turkey.

Even as rebels took control of Damascus, fighting flared between Turkey and the Kurds in the northeast of Syria, centered on Manbij, a Kurdish-controlled city near the Turkish border. At least 22 members of the Syrian Democratic Forces were killed in and around Manbij, and 40 others were wounded, according to the Kurdish group.

The Syrian National Army

This umbrella group includes dozens of groups with different beliefs. It receives funding and arms from Turkey, which has long been focused on expanding a buffer zone along its border with Syria to guard against the activities of Kurdish militants based in the region that it sees as a threat.

Turkey wants to create an area where it can resettle some of the three million refugees who have fled Syria and are living within its borders. But it has struggled to harmonize the ragtag groups that make up the Syrian National Army.

The group is largely composed of the dregs of the Syrian civil war, including many fighters whom the United States had rejected as criminals and thugs. Some received training from the United States early in the war, but most were dismissed as too extreme or too criminal. Most have no clear ideology and had turned to Turkey for a paycheck of about $100 a month when the group was formed.

On Monday, there were fierce battles in the northern city of Manbij between the Syrian National Army, supported by Turkish airstrikes and artillery, and the Kurdish Syrian Democratic Forces.

According to the Syrian Observatory for Human Rights, a war monitoring group based in Britain, the city was captured by the Syrian National Army. A spokesperson for the Syrian Democratic Forces said fighters with the Syrian National Army had taken only 60 percent of the city. The claims could not be independently verified.

The Druse militia

Syria’s Druse minority is concentrated in Sweida, an area in the southwest of Syria that has seen rare antigovernment demonstrations over rising costs of living, and many Druse men have refused military service. This week, Druse fighters joined the push to topple the Assad regime, launching an offensive in the southwest and clashing with government forces, according to media reports.

The Druse fighters are part of a newly formed group of Syrian rebels, which includes fighters from other backgrounds, working under the name the “Southern Operations Room.”

The Druse are a religious group that practices an offshoot of Islam, developed in the 11th century, that contains elements of Christianity, Hinduism, Gnosticism and other philosophies. There are more than one million Druse across the Middle East, mostly in Syria and Lebanon, with some also in Jordan and Israel.

The Islamic State in Iraq and Syria

The Islamic State in Iraq and Syria, better known as ISIS, seized vast stretches of territory in Syria and Iraq in 2014, establishing a brutal regime before it was beaten back by a U.S.-led coalition. Now its members are largely in hiding.

Lately, there have been signs of the group’s resurgence in Syria amid wider instability in the region. The Pentagon warned in July that Islamic State attacks in Syria and Iraq were on track to double compared to the previous year. The group has repeatedly tried to free its members from prisons and has maintained a shadow governance in parts of northeastern Syria, the U.S. said.

President Biden announced on Sunday that the U.S. military has been conducting airstrikes in Syria to keep the Islamic State from reasserting itself in the power vacuum created by Mr. al-Assad’s ouster.

The United States has about 900 troops in Syria to help contain and defeat what remains of ISIS there. The U.S. has not given a date for ending its presence in the country, saying it was contingent on conditions within the war-torn country. Those conditions have now changed dramatically.

“We’re cleareyed about the fact that ISIS will try to take advantage of any vacuum to reestablish its capability, to create a safe haven,” Mr. Biden said. “We will not let that happen.”

Now, after a lightning advance by rebels and the rapid-fire collapse of Mr. al-Assad’s government, great powers — albeit with different ones in ascendence — are jockeying for advantage within Syria’s borders. For the first time in years, the skies are empty of Syrian and Russian bombers — but airstrikes by Israel, Turkey and the United States continue.

Here is a look at the foreign countries that have been present in Syria — often operating through local allies — and what they stand to gain and lose from the end of the Assad regime.

Turkey

Turkey has two primary concerns in Syria: Kurds and refugees.

Eastern Syria is home to a sizable ethnic Kurdish population, which the Turkish government sees as allied with Kurdish separatist groups in Turkey. The country is also hosting nearly four million Syrian refugees who fled persecution by the Assad government, and President Recep Tayyip Erdogan would like them to return home.

Turkey, which was once the seat of the vast Ottoman Empire that included much of Syria, has backed an array of different rebel groups that hold territory along the Syrian-Turkish border. One of those groups, Hayat Tahrir al-Sham, which led the offensive that toppled Mr. al-Assad, had benefited from Turkey’s military presence in the area.

It is unclear whether Turkey approved the group’s decisive offensive.

However, Ankara’s closest ties are with the Syrian National Army, which has functioned almost as a proxy force for Turkey — in the past, the group’s leadership has said it received funding and weapons — and in turn it has pushed the Syrian Kurds, whom the Turks view as a security threat, back from the border. Just in the last few days, as the rebels led by Hayat Tahrir al-Sham took control of the capital, Damascus, fighting flared between the Syrian National Army and the Kurds in northeastern Syria, centered on Manbij, a Kurdish-controlled city near the border with Turkey. Turkey supported the Syrian National Army with airstrikes.

Turkey now seems to be the foreign power with the most access and influence with the armed groups now in charge and in a prime position to pursue its own goals in Syria. That could mean further attacks against the Syrian Kurds, and the return of refugees who are currently in Turkey.

Israel

Israel has fought three wars with Syria, and has had many more armed confrontations. It holds much of the mountainous territory in the southwest of Syria known as the Golan Heights, an annexation that is not recognized by the United Nations and many other countries.

During the civil war, Israel regularly conducted airstrikes against Iran’s and Hezbollah’s weapons stores and personnel in Syria. In April, it bombed an Iranian Embassy building in Damascus, killing senior Iranian military and intelligence officials

Within hours of the fall of the Assad regime, Israel moved troops into the Golan Heights, advancing beyond the demilitarized zone in its first overt entry into Syrian territory since the 1973 October War.

Israeli officials also said that their country was striking weapon stockpiles in Syria, including chemical weapons and long-range missiles and rockets, to prevent Syria’s new leaders from potentially attacking Israel in the future.

The Syrian Observatory for Human Rights, an independent group based in Britain that has tracked the civil war in Syria for years, said that it had documented 322 Israeli strikes in Syria since Sunday, when President Bashar al-Assad fled the country. It said the strikes had targeted “warehouses, aircraft squadrons, radars, military signal stations, and numerous weapons and ammunition depots,” including some as recently as Tuesday morning.

Gideon Saar, Israel’s foreign minister, told reporters on Monday that the leaders of Syria’s rebels “are people with an extreme ideology of radical Islam.” Israeli forces are destroying the weapons “in order that they don’t fall in the hands of extremists,” he added.

Israel has touted its actions against Hamas and Hezbollah as instrumental in the overthrow of the Assad government. But it is not clear that a new government in Damascus, dominated by militant Islamists, will make Israel any safer.

Iran

Iran’s relationship with Syria dates back almost 50 years, when Syria’s president at the time, Hafez Assad, supported Iran in its eight-year war with Iraq. As Iran built a network of like-minded groups across the Middle East as a counterweight against the United States and Israel, Syria was the only state to become part of what Iran called its “Axis of Resistance.”

Syria became Iran’s main overland supply route to transport weapons to Hezbollah in Lebanon. In return, Iran sent military advisers to support the Assad regime during the civil war, along with fighters from its ally Hezbollah and two brigades under the command of Iran’s Quds Forces that was made up of refugees from Pakistan and Afghanistan who had fled to Iran.

With Mr. al-Assad forced to flee Syria, Iran will lose much of its military leverage in Lebanon and Syria. Its hopes for an “Axis of Resistance” that reached the Mediterranean have unraveled — at least for now.

Russia

The Russian relationship with Syria dates to the days of the Soviet Union. At the end of the Cold War, with the United States asserting its presence in Arab countries, Russia saw the Assad government as a crucial ally in the Middle East, one that could provide a counterweight to the American presence.

During the Syrian civil war, Russia made it a priority to keep its ally in power. It also saw the Syrian leader as a bulwark against Islamist extremism from Al Qaeda and the Islamic State. Russia sold weapons to the Assad government, deployed fighters from Russia’s Wagner group, expanded its naval base in Tartus, Syria, and opened an air base near Damascus.

With the demise of the Assad regime, Russia could lose much of its influence in Syria, but analysts say it probably will try to keep its Tartus base, which is its only Mediterranean port for its Black Sea fleet It is making conciliatory gestures toward the rebel forces who now control the country, and has said it is too soon to make any decisions about the fate of its military bases in Syria.

United States

The U.S.-Syria relationship has never been particularly friendly. The United States severed diplomatic relations in 1967 during the Arab-Israeli war, and placed Syria on its list of state sponsors of terrorism in 1979.

The main U.S. interest in Syria now is the defeat of the Islamic State, which maintains a presence in the northeastern and central parts of the country. In 2019, during Donald Trump’s first term as president, he pulled most U.S. forces out of Syria, but about 1,000 U.S. Special Operations troops remain, and they work closely with Syrian Kurdish troops trained by the United States.

President Biden said on Sunday that the U.S. military has been conducting airstrikes in Syria to keep the Islamic State from reasserting itself in the power vacuum created by Mr. al-Assad’s ouster. He said the United States would support the region “should any threat arrive from Syria during this period of transition.”

“We’re cleareyed about the fact that ISIS will try to take advantage of any vacuum to re-establish its capability, to create a safe haven,” Mr. Biden said. “We will not let that happen.”

Additional reporting by Jack Nicas.

Some rushed to a notorious prison on the outskirts of Damascus, the capital, desperate to find loved ones who had disappeared under Mr. al-Assad’s brutal reign. Others clambered on top of cars and screamed curses at the Assad family, words that days ago could have meant a death sentence.

By day’s end, with Mr. al-Assad and his family having fled on a plane to his ally Russia, thousands of Syrians had converged at Umayyad Square in the city center to revel in the fall of the regime and their newfound, if uncertain, sense of freedom.

“We’re shocked; all of us are just shocked,” one woman, Shahnaz Sezad, 50, said. “It’s as if we’re all coming back to life after a nightmare.”

She watched, tears welling up, as a scene unimaginable just days ago played out in front of her. One rebel shouted into a microphone: “The Syrian people want to execute Bashar! The Syrian people want to execute Bashar!” A deafening “paw-paw-paw” of gunfire sounded as others shot into the air.

Across Damascus, rebels and residents alike were reckoning with the beginning of a new chapter in Syria. The only certainty seemed to be that the city was free from the brutal reign of the Assad family, which ruled the country with an iron fist for more than 60 years. Remnants of Mr. al-Assad’s regime were scattered across the city; the posters with his face, once ubiquitous, were torn off walls and ripped to shreds.

As the rebel coalition that swept into Damascus suddenly found itself in charge of the Syrian capital, a sense of unease mingled with the disbelief. The precariousness of their newly won freedom was not lost on them. No one — not residents, not rebels — seemed certain of what might come next, beyond the daunting task of reconciling the deep ethnic, sectarian and religious divisions that racked the country under Mr. al-Assad’s rule.

The rebel leadership announced in a statement on Monday that its forces were “about to finish controlling the capital and preserving public property.” The rebels said they were forming a transitional government, and called on public sector employees to return to work.

The statement did not name the leader of the transitional government, but local news reports said it would be Mohammed al-Bashir, who was previously the head of a rebel-run administration in northwestern Syria.

The rebels’ leader, Ahmed al-Shara, formerly known as Abu Mohammed al-Jolani (he has shed the nom de guerre he had used throughout Syria’s long civil war), also made a conciliatory gesture toward Syria’s government institutions and their staffs on Monday.

“We can’t dispense with the previous state,” Mr. al-Shara told Mr. al-Assad’s prime minister, who stayed behind when the president fled, according to a video clip of the meeting posted by the rebel leaders. The rebels’ experience governing has been limited to the patch of territory they held before toppling the government.

In a video of him speaking at the ancient Umayyad mosque in Damascus, Mr. al-Shara can be heard lauding the rebels’ surprisingly rapid victory. “By God’s grace,” he says, “this land of Syria was liberated within 11 days from its north to its south, from its east to its west.”

Late Monday morning, Victor Dawli, 59, stood in his apartment’s entryway in Old Damascus, the centuries-old city center of winding, narrow alleys. As a truck carrying rebels passed, Mr. Dawli waved, a cigarette in hand. One fighter, clutching his rifle and hunched over in the bed of the truck, nodded.

Mr. Dawli’s neighborhood, Babsharqi, is home mostly to Christians, many of whom had supported the Assad government and now fear that they could face retribution. Since Mr. al-Assad’s flight abroad on Sunday as rebels seized the capital, many people in the neighborhood have been walking a tightrope. Some have kept their heads down and stayed inside their homes. Others, like Mr. Dawli, say they secretly supported the rebels from the start.

When one neighbor passed by, Mr. Dawli shouted to him, “Good morning, congratulations!” The man gave him a blank stare and then hurried down a nearby alleyway. “There are people who are scared,” Mr. Dawli said. “You tell them congratulations, and they feel uneasy.”

Across the capital, opposition forces appeared to be trying to restore a sense of order to the city. Small groups of rebels in mismatched camouflage stood outside government buildings and banks blocking people from entering and ransacking them as many had done a day earlier. Other rebels wearing plain clothing and carrying rifles directed traffic at major intersections.

Still others drove through the streets to marvel at the capital, or to track down relatives they had not seen in over a decade.

One rebel, Mohammad Bakir, 41, sat in the back of a car, his rifle tucked between his knees. He had been stuck for about an hour in traffic, one of thousands of people trying to get to Sednaya, the prison on the outskirts of Damascus that had come to symbolize terror and death under the Assads’ regime.

Mr. Bakir said that his mother, brother and cousin had all disappeared in 2012 in Idlib Province after taking to the streets to protest the government. He had not heard any news about them in the 12 years since.

“Seizing the city is a joy — we are joyous,” Mr. Bakir said, shouting over the din of car horns. “But the real victory will be when I find my family.”

By the time he arrived at the prison, thousands of families had converged upon it, touring its now-empty cells and desperately asking rebels for news of the prisoners released on Sunday, and whether any others remained. Some men with pickaxes tore into the cement floor, hoping to find the secret prison cells they were convinced were hidden underground and still holding prisoners.

A few miles from the border, the body of a man in military uniform lay sprawled on the ground next to an abandoned pickup. Down the road from one Syrian military base, a convoy of 10 rebel vehicles sped down the highway. They drove four-wheel-drive vehicles — their doors and windows caked in mud as camouflage — and Syrian military vehicles armed with rockets that once belonged to the Assad government.

There were signs of the lawlessness that many fear might seize the country in the coming days or weeks if the rebel coalition was unable to maintain order.

The storefront windows of a duty-free shop just across the border from Lebanon were smashed, while bottles, chocolates and bags of snacks were strewed across the floor. Windshields and windows of dozens of abandoned cars along the roads were broken, their doors flung open.

Two young men fiddled with the wires beneath one abandoned truck, an apparent attempt to jump-start the vehicle. Nearby, one young man stood in front of an abandoned tank taking a selfie. He picked up his toddler and placed him on top of the tank for a photo. Then he told him to hold his fingers up in a V — the sign for victory.

Mr. Hassan, who was the head of the Air Force Intelligence Directorate, and Mr. Mahmoud, a brigadier general in the Air Force’s intelligence unit, “sought to terrify, intimidate and repress any opposition, or perceived opposition, to the regime,” according to the indictment, which was filed under seal last month in federal court in Chicago.

The indictment was made public the day after Syrian rebels overthrew the government of President Bashar al-Assad of Syria. Mr. Hassan and Mr. Mahmoud would need to be flown to federal court in Chicago to stand trial, but the charges provide the legal mechanism for American law enforcement to take custody of the men, if they can be found.

Mr. al-Assad, an authoritarian leader known for his brutal tactics during a 13-year civil war, has already fled to Russia, which, along with Iran, had helped keep him in power.

As top leaders under Mr. al-Assad, Mr. Hassan oversaw a crackdown on Syrian citizens in which a ruthless system of detention and torture flourished, and Mr. Mahmoud, as a brigadier general in the Air Force Intelligence unit, was in charge of the prison at the military air base in the Mezzeh neighborhood of Damascus as well as operations at the base.

Along with unnamed co-conspirators, Mr. Hassan and Mr. Mahmoud “committed the war crime of knowingly and intentionally conspiring to commit cruel and inhuman treatment,” according to the indictment. The men intended to inflict “serious physical abuse upon victims within their custody or control, namely U.S. citizens and other detainees” held at the Mezzeh prison, where investigators said both men had offices.

The indictment describes the torture that Syrian military officials doled out from 2012 to 2019. That included electrocution and pulling out the toenails of prisoners, as well as burning them with acid and regularly beating them.

The men were instrumental in helping Mr. Assad silence dissent, using torture — and fear of it — to maintain his government for more than a decade. His rule came to an end days ago, when rebels seized the country’s largest city, Aleppo, and the capital, Damascus, and toppled Mr. Assad’s government. The rebels freed prisoners in the country, many of them thought to be innocent civilians.

Both Mr. Hassan and Mr. Mahmoud are well known to human rights advocates and the American government. In 2012, the United States imposed sanctions on Mr. al-Assad and his inner circle, including Mr. Hassan, for committing acts of violence against civilians.

In mid-November, three days before a grand jury returned the indictment against the men, the State Department said that it had restricted Mr. Mahmoud’s ability to travel “due to his involvement in gross violations of human rights, namely torture or cruel, inhuman or degrading treatment or punishment.”

A spokesman for the Chicago U.S. attorney’s office did not respond to a request for comment about why prosecutors waited more than 20 days to unseal the indictment.

Prosecutors in Chicago have been investigating Mr. Hassan and others since 2018, when the Justice Department opened a case related to the detention and killing of an American aid worker named Layla Shweikani. F.B.I. agents traveled to Europe and the Middle East to interview witnesses, including the man who may have buried Ms. Shweikani.

The indictment does not name Ms. Shweikani, who was held imprisoned on the outskirts of Damascus for nearly a year at three detention facilities known for their use of torture: a facility at the Mezzeh airport, the Adra civilian prison and the Sednaya military prison.

Dina Kash, an F.B.I. witness who was detained at Mezzeh prison, said in an interview that investigators wanted names of fellow detainees and information about how they were treated. Syrian guards beat her, knocking out her teeth. She was forced to listen to the screams of other prisoners being tortured. Guards killed her husband.

“The investigators focused on the people that interrogated me and the Assad regime, intelligence operatives and officials that were involved in my family’s arrest, including Hassan,” Ms. Kash said.

Mouaz Moustafa, the executive director of the Syrian Emergency Task Force, said now was the time for the United States to hold responsible those officials who had subjected American citizens and countless others to detention and torture. “Now it is our time to catch these criminals and bring them to the United States for trial,” said Mr. Moustafa, who added that he was traveling to Syria to help law enforcement agencies gather human remains and documents from the prisons.

The director of the F.B.I., Christopher A. Wray, in a statement, vowed to hold the men to account. “Hassan and Mahmoud allegedly oversaw the systematic use of cruel and inhumane treatment on perceived enemies of the Syrian regime, including American citizens,” he said.

The indictment does not mention Austin Tice, an American abducted in Syria in 2012. Syria never acknowledged holding Mr. Tice, but American officials are hopeful that he survived what would have amounted to a grueling stretch inside the prison system.

American officials are confident that Mr. Tice was held by the Syrians early in his abduction. Investigators learned that he had initially been taken to a prison in Damascus and was seen by a doctor, according to two people familiar with the matter. Mr. Tice managed to escape for about a week but was recaptured, the people said.

In May, U.S. officials informed the family of Majd Kamalmaz, a therapist from Texas, that he died in Syria after disappearing there in 2017. Like the case of Mr. Tice, Syria never acknowledged holding Mr. Kamalmaz, and there was little information about his whereabouts.

Mr. Moustafa said he and his research team strongly suspected that Mr. Kamalmaz was imprisoned, at least for some of his time in Syria, at the Mezzeh air base.

Facing a new 11th-hour Middle East crisis before leaving power, the Biden administration hopes to keep the lid on a Pandora’s box of threats that could emerge from a post-Assad Syria. Among them are a resurgence of anti-American terrorists, new dangers for neighboring Israel and a spasm of violence that could drive more refugees from the country.

U.S. officials have been speaking to their counterparts in Turkey in recent days. Secretary of State Antony J. Blinken talked with Hakan Fidan, the foreign minister of Turkey and a former intelligence chief, on Saturday as the militias were moving quickly toward Damascus, the capital of Syria.

Mr. Blinken “emphasized the importance of protecting civilians, including members of minority groups, across Syria,” according to a State Department summary of the call.

It was clear Mr. Blinken intended for Mr. Fidan to convey that message to the militias.

While the United States sees Turkey as a potentially helpful partner, given its close rebel ties, Biden officials are also wary of its intentions toward U.S.-backed Kurdish fighters who have battled the Islamic State in northeastern Syria.

On Sunday, Defense Secretary Lloyd J. Austin III spoke with his Turkish counterpart, Yasar Guler, in part “to avoid any risk to U.S. forces and partners, and the Defeat-ISIS Mission,” according to a summary of the call from the Pentagon.

The conversation followed Turkish attacks on the Kurdish-led Syrian Democratic Forces that the group said killed at least 22 of its members. Turkish officials say those Kurdish fighters are aligned with Kurdish nationalist militants inside their country.

The Biden administration is intensifying talks over Syria with other allies in the region.

The White House said on Monday that Jake Sullivan, the national security adviser, would fly to Israel this week to speak to officials there about the related situations in Gaza, Syria, Lebanon and Iran.

The rapid fall of the Assad government surprised both Israel and the United States. Israeli troops crossed into Syria over the weekend and quickly bolstered defenses in the Golan Heights, which Israel had annexed from Syria. Israel also conducted airstrikes on chemical weapons stockpiles in Syria, Israeli officials said.

The State Department spokesman, Matthew Miller, told reporters on Monday that Biden officials “have a number of ways of communicating” with rebel leaders — “sometimes directly with various groups, sometimes with intermediaries, either inside Syria or outside Syria.”

Roger D. Carstens, the U.S. special envoy for hostage affairs, is already in Beirut as part of a renewed effort to win the freedom of Austin Tice, an American journalist who disappeared in Syria in 2012 and whom President Biden believes to be alive.

Mr. Carstens’s mission is “to find out where Austin Tice is and get him home as soon as possible,” Mr. Miller said.

“We have reason to believe that he is alive,” Mr. Miller said, without providing details.

The United States has been wary of Hayat Tahrir al-Sham and its 42-year-old leader, Abu Mohammed al-Jolani, ever since President Barack Obama designated its earlier incarnation a terrorist group. U.S. officials say they are closely watching to see whether the organization displays traits of a terrorist group or whether it has changed.

“We will be closely monitoring developments as they unfold and engaging with our partners in the region,” Mr. Blinken said in a statement on Sunday. “We have taken note of statements made by rebel leaders in recent days, but as they take on greater responsibility, we will assess not just their words, but their actions.” He specifically cited respect for human rights and the protection of civilian noncombatants.

David Lammy, the foreign secretary of Britain, said the same thing on Monday. At least one British cabinet official has suggested his government could lift its terrorist designation on the group under the right circumstances.

The U.S. process for a full lifting of the same designation could take weeks or months, once a decision is made.

A senior U.S. official said on Sunday that it was too early to discuss whether the United States might remove its sanctions on Hayat Tahrir al-Sham. But the official suggested, in an echo of Mr. Blinken’s statement, that the group would have to earn such a reprieve with tangible action.

Colin P. Clarke, a counterterrorism analyst at the Soufan Group, a security consulting firm based in New York, called any softening of the U.S. position toward Mr. Jolani “a huge risk.”

“Jolani has done an amazing job at rehabbing his image; he’s presenting himself as a modern-day revolutionary cut from the same cloth as Che Guevara, and this is resonating in many parts of the Middle East and further abroad,” Mr. Clarke said. “However, under his rule, northwestern Syria has still been a harsh place where critics are silenced, tortured, jailed and disappeared.”

He noted that the United States still maintains a bounty of up to $10 million on Mr. Jolani’s head.

“Assad is a brutal dictator, but that doesn’t make Jolani more palatable,” Mr. Clarke added. “Neither of these individuals should be running Syria, but U.S. policy needs to deal with realities on the ground and not ideal scenarios.”

The U.S. government broke off diplomatic relations with Mr. Assad and his government in 2012, as the uprising that began the previous year spiraled into a devastating civil war.

Robert Ford, the U.S. ambassador then, pushed the Obama administration to designate the Al Nusra Front, the precursor to Hayat Tahrir al-Sham, a terrorist group because its fighters set off two suicide car bombs in Damascus in December 2011. The explosions, outside the offices of a security agency, killed at least 44 people, most of them civilians, according to the Syrian government.

Mr. Ford said in an interview on Monday that he would now advise the Biden administration to consider taking Hayat Tahrir al-Sham off the terrorist list because it appears to have adopted more moderate ideas and tactics.

Mr. Ford said the group had broken from the Islamic State and Al Qaeda years ago and had fought both organizations. He also said Hayat Tahrir al-Sham tolerated Christian practices and had allowed Christians to rebuild churches in the Idlib region, the part of Syria that the group has controlled and governed in the late stages of the civil war.

Mr. Ford added that the Biden administration should ensure it has channels to the main players, and that it should encourage its partners, notably Kurdish militias and political groups in the northeast, to engage in any emerging political process.

The Pentagon has kept 900 U.S. troops in northeast Syria, where they work with Kurdish fighters in operations against the Islamic State. But the Kurds are trying to fend off attacks by armed groups backed by Turkey.

“Instead of trying to manage a political process or support,” Mr. Ford said, “it’s much better to engage at a bit of a distance and be encouraging.”

Senior Pentagon officials have said U.S. troops will remain in Syria — at least for now — to continue their efforts to prevent the Islamic State from returning.

Daniel Shapiro, the deputy assistant secretary of defense for the Middle East, said at a security conference in Manama, Bahrain, that the Pentagon would push for the Islamic State’s “enduring defeat, to ensure the secure detention of ISIS fighters and the repatriation of displaced persons.”

American warplanes carried out airstrikes on Islamic State sites in central Syria on Sunday, hitting more than 75 targets, U.S. officials said.

“There should be no doubt — we will not allow ISIS to reconstitute and take advantage of the current situation in Syria,” said Gen. Michael Erik Kurilla, the head of U.S. Central Command, which oversees operations in the Middle East. “All organizations in Syria should know that we will hold them accountable if they partner with or support ISIS in any way.”

Iran-backed militias in Iraq and Islamic State militants in Syria have occasionally attacked American troops at a handful of bases in the region.

But as the Biden administration focused on Russia’s invasion of Ukraine and a potential future conflict with China, the counter-ISIS mission in Syria became something of a back-burner issue.

During his first administration, President-elect Donald J. Trump sought to withdraw American forces from Syria but was talked out of it by senior Pentagon officials, including Gen. Mark A. Milley, the chairman of the Joint Chiefs of Staff at the time.

Eric Schmitt contributed reporting.