BEIRUT, Lebanon — American-backed forces have barely begun to clear the land mines from Raqqa after pushing the Islamic State from the city, the de facto capital of its self-declared caliphate.
But the militants’ defeat there is already setting the stage for a new round of conflict and instability in Syria’s long civil war.
Fleeing jihadists are already regrouping in remote areas, rearming with the help of desert smugglers. Tensions are brewing over who will ultimately control Raqqa, where American-backed Kurdish and Arab forces declared victory on Tuesday.
And as the Islamic State threat wanes, the Syrian government is expected to return its military attention to the Syrian rebels, intensifying the kind of bombardment that has led to mass civilian casualties, with no sign of a political solution in sight.
To defeat Islamic State, myriad international and Syrian combatants — many of them sworn enemies — banded together or put their conflicts on the back burner. Now, even as they close in on Islamic State’s last territories near the Iraqi border, their submerged tensions are rising to the surface.
Raqqa was taken by an American-backed militia made up of Syrian Kurds and Arabs. Soon after, celebrating Kurdish fighters raised flags adorned with the face of Abdullah Ocalan, a Kurdish militant leader. Many of Raqqa’s Arab residents, who considerMr. Ocalan a terrorist, were appalled. Some are calling the Kurds new occupiers.
Others downplayed the prospect of tensions between Arabs and Kurds. The American-backed militia says it will soon hand formal control of Raqqa to a civilian city council made up of representative local residents.
“We are all on the same ship,” said Hassan Mohammad Ali, a Raqqa resident involved in rebuilding the local government. Both Arabs and Kurds want “a democratic, pluralistic Syria,” he said, and would not try to impose their will on each other.
But the Syrian government has no intention of letting that arrangement stand.
The government of President Bashar al–Assad now controls most of the country, having taken back much of the territory once held by rebel groups who took up arms after the government cracked down on protests in 2011.
Backed by Russia and Iran, Mr. Assad has vowed to recapture all of Syria, including Raqqa and the areas beyond it where the Kurds have established a semiautonomous zone.
It remains unclear how far the United States would go to stop him.
Pentagon officials say that, for now, the American military will continue to defend areas like Raqqa, which American-backed forces reclaimed from the Islamic State. In June, the military shot down two Syrian drones that American officials said were threatening American-backed troops.
That posture has not changed, the officials said, and Syria experts say they expect it to continue for the next few months. What happens after that — and how willing the United States is to become engaged in a war against the Assad government and its international backers — is an open question.
“The issue of self-defense will certainly continue as long as the fight against ISIS continues,” said Andrew J. Tabler, a Syria expert with the Washington Institute for Near East Policy. “But what goes on after that with the political process, I don’t know.”
Trump administration officials acknowledge privately that the military campaign in Syria has by far outstripped the diplomatic campaign, to the point now where there is no real plan for what to do in a post-Islamic State Syria.
That is not for lack of trying by John Kerry, the secretary of state under President Barack Obama who sought a political solution for a post-Islamic State Syria, and Brett H. McGurk, the Trump administration’s point man on Syria.
With the Islamic State far from defeated the American-backed coalition is “not quite ready to take their foot off the gas pedal yet,” said Eric Robinson, an analyst with the RAND Corporation.
The militant group still controls close to 4,000 square miles of territory on either side of the Iraq-Syria border, harboring an estimated 6,000 to 10,000 fighters.
As its fighters are pushed out of their strongholds, many are going underground, vowing to continue their battle as hit-and-run insurgents. There are growing pockets of them in the eastern desert areas of at least three Syrian provinces, including many hiding in areas under government control, according to fighters and residents of the areas.
But thousands of Islamic State fighters have been allowed to simply hand in their weapons and go free under an odd loophole that has become a trademark of this conflict. Just before the final assault on a militant-controlled town or village, it is not unusual to see lines of buses pulling up, loading hundreds of fighters and their families, and driving them off the battlefield, sometimes to other Islamic State-controlled territory.
Both the Syrian government forces and the American-backed militias have afforded this privilege mainly to Syrian militants, some of whom say they were forced to join the Islamic State, but also to foreigners who came to Syria to wage jihad.
While the practice has truncated battles, saving lives on both sides, it has also had a balloon effect, squeezing fighters out of Raqqa, for instance, and inflating their numbers in Deir al-Zour, a province along the Iraqi border that is now the site of the biggest battle against the Islamic State.
In Raqqa, at least four people, Raqqa residents or aid workers, said they had seen fighters boarding the buses. Two aid workers said at least 15 buses had departed for Deir al-Zour.
Others move on to government-held areas, like the southern province of Sweida. Fleeing Syrian Islamic State fighters are turning themselves in to the government there daily, says Nour al-Shami, a former Sweida resident who lives in exile in Turkey.
But then, he said, many of the fighters then slip away to the caves of province’s eastern badlands, and buy weapons from smugglers, who have in some cases bought them from government forces.
Fugitive Islamic State fighters are also gathering near the Palmyra ruins, in the north, that were retaken twice from Islamic State by pro-government forces. One fighter, reached by text message, said he now belongs to a group called Soldiers of the Caliphate that hopes to recruit foreign fighters from Islamic State and rival Qaeda-linked groups to continue the struggle.
The fighter, who gave only a first name, Yehya, said he was with scores of others, mainly foreigners who preferred to fight to the death in Syria than risk arrest by heading home to Central Asia, Europe and other places.
“What choice do they have?” he said.
Six years of war has left Syria a wreck: whole cities have been laid waste, the economy is devastated, an estimated 100,000 people remain in government detention or disappeared after being arrested. The government is heavily beholden to Iran and Russia, which saved Mr. Assad’s rule in exchange for unprecedented influence.
Government warplanes are bombing Idlib Province, where hundreds of thousands of civilians are trapped along with rebel groups and hard-core Qaeda-linked jihadists.
Mr. Assad has made virtually no concessions even to his unarmed, political opponents, whose street protests calling for more rights and an end to corruption started the unrest in 2011. That leaves, as the Syria analyst Peter Harling put it recently, “minimal prospects of reform, reconciliation or reconstruction, let alone closure.”
Any prospects for a coherent, unified reconstruction are complicated by the fact that the United States and its allies are still refusing to work with Mr. Assad, and the government rejects the presence of any groups that don’t work through it.
In Raqqa, international aid groups, considered illegal by the Assad government, are trying to rejuvenate the mostly agricultural economy, telling residents to “forget the fighting and remember the shovel,” as one aid worker put it.
Members of the councils set up by the Syrian Democratic Front to rebuild civilian government say they want to prevent the government from returning to power in Raqqa unless there is deep reform that gives them a greater say over their affairs, an unlikely prospect.
“We have no plans to give up Raqqa to anyone, not to the regime, not to anyone,” said Nazmi Mohammad, a member of the council that is to soon take over the city’s governance. “We are not scared of the regime. The regime is not stronger than Islamic State.”