CAIRO — In Syria’s largest city, Aleppo, rebels aligned with Al Qaeda control the power plant, run the bakeries and head a court that applies Islamic law. Elsewhere, they have seized government oil fields, put employees back to work and now profit from the crude they produce.
Across Syria, rebel-held areas are dotted with Islamic courts staffed by lawyers and clerics, and by fighting brigades led by extremists. Even the Supreme Military Council, the umbrella rebel organization whose formation the West had hoped would sideline radical groups, is stocked with commanders who want to infuse Islamic law into a future Syrian government.
Nowhere in rebel-controlled Syria is there a secular fighting force to speak of.
This is the landscape President Obama confronts as he considers how to respond to growing evidence that Syrian officials have used chemical weapons, crossing a “red line” he had set. More than two years of violence have radicalized the armed opposition fighting the government of President Bashar al-Assad, leaving few groups that both share the political vision of the United States and have the military might to push it forward.
Among the most extreme groups is the notorious Al Nusra Front, the Qaeda-aligned force declared a terrorist organization by the United States, but other groups share aspects of its Islamist ideology in varying degrees.
“Some of the more extremist opposition is very scary from an American perspective, and that presents us with all sorts of problems,” said Ari Ratner, a fellow at the Truman National Security Project and former Middle East adviser in the Obama administration. “We have no illusions about the prospect of engaging with the Assad regime — it must still go — but we are also very reticent to support the more hard-line rebels.”
Syrian officials recognize that the United States is worried that it has few natural allies in the armed opposition and have tried to exploit that with a public campaign to convince, or frighten, Washington into staying out of the fight. At every turn they promote the notion that the alternative to Mr. Assad is an extremist Islamic state.
The Islamist character of the opposition reflects the main constituency of the rebellion, which has been led since its start by Syria’s Sunni Muslim majority, mostly in conservative, marginalized areas. The descent into brutal civil war has hardened sectarian differences, and the failure of more mainstream rebel groups to secure regular arms supplies has allowed Islamists to fill the void and win supporters.
The religious agenda of the combatants sets them apart from many civilian activists, protesters and aid workers who had hoped the uprising would create a civil, democratic Syria.
When the armed rebellion began, defectors from the government’s staunchly secular army formed the vanguard. The rebel movement has since grown to include fighters with a wide range of views, including Qaeda-aligned jihadis seeking to establish an Islamic emirate, political Islamists inspired by the Muslim Brotherhood and others who want an Islamic-influenced legal code like that found in many Arab states.
“My sense is that there are no seculars,” said Elizabeth O’Bagy, of the Institute for the Study of War, who has made numerous trips to Syria in recent months to interview rebel commanders.
Of most concern to the United States is the Nusra Front, whose leader recently confirmed that the group cooperated with Al Qaeda in Iraq and pledged fealty to Al Qaeda’s top leader, Ayman al-Zawahri, Osama bin Laden’s longtime deputy. Nusra has claimed responsibility for a number of suicide bombings and is the group of choice for the foreign jihadis pouring into Syria.
Another prominent group, Ahrar al-Sham, shares much of Nusra’s extremist ideology but is made up mostly of Syrians.
The two groups are most active in the north and east and are widely respected by other rebels for their fighting abilities and their ample arsenal, much of it given by sympathetic donors in the gulf. And both helped lead campaigns to seize military bases, dams on the Euphrates River and the provincial capital of Raqqa Province in March, the only regional capital entirely held by rebel forces.
Nusra’s hand is felt most strongly in Aleppo, where the group has set up camp in a former children’s hospital and has worked with other rebel groups to establish a Shariah Commission in the eye hospital next door to govern the city’s rebel-held neighborhoods. The commission runs a police force and an Islamic court that hands down sentences that have included lashings, though not amputations or executions as some Shariah courts in other countries have done.
Nusra fighters also control the power plant and distribute flour to keep the city’s bakeries running.
While many residents initially feared them, some have come to respect them for providing basic services and working to fill the city’s security vacuum. Secular activists, however, have chafed at their presence. At times, Nusra fighters have clashed with other rebels who reject their ideology.
In the oil-rich provinces of Deir al-Zour and Hasaka, Nusra fighters have seized government oil fields, putting some under the control of tribal militias and running others themselves.
“They are the strongest military force in the area,” said the commander of a rebel brigade in Hasaka reached via Skype. “We can’t deny it.”
But most of Nusra’s fighters joined the group for the weapons, not the ideology, he said, and some left after discovering the Qaeda connection.
“Most of the youth who joined them did so to topple the regime, not because they wanted to join Al Qaeda,” he said, speaking on the condition of anonymity for fear of retaliation.
As extremists rose in the rebel ranks, the United States sought to limit their influence, first by designating Nusra a terrorist organization, and later by pushing for the formation of the Supreme Military Council, which is linked to the exile opposition group, the Syrian National Coalition.
Although led by an army defector, Gen. Salim Idris, the council has taken in the leaders of many overtly Islamist battalions. One called the Syrian Liberation Front has been integrated nearly wholesale into the council; many of its members coordinate closely with the Syrian Islamic Front, a group that includes the extremist Ahrar al-Sham, according to a recent report by Ms. O’Bagy, of the Institute for the Study of War.
A spokesman for the council, Louay Mekdad, said that its members reflected Syrian society and that it had no ties to Nusra or other radical groups. “The character of the Syrian people is Islamic, but it is stupid to think that Syria will turn into Afghanistan,” he said. “That’s just an excuse for those who don’t want to help Syria.”
The Obama administration has said it needs more conclusive information before it acts on the Syrian government’s reported use of chemical weapons. It remains unclear whether such action would translate to increased support for the rebels.
In the past, United States officials saw the Islamist groups’ abundant resources as the main draw for recruits, said Steven Heydemann, a senior adviser at the United States Institute of Peace, which works with the State Department.
“The strategy is based on the current assessment that popular appeal of these groups is transactional, not ideological, and that opportunities exist to peel people away by providing alternative support and resources,” he said.
Mr. Heydemann acknowledged, however, that the current momentum toward radicalism could be hard to reverse.
The challenge, he said, was to end the conflict before “the opportunity to create a system of governance not based on militant Islamic law is lost.”
Emile Hokayem, a Middle East analyst at the International Institute for Strategic Studies, framed the rebels’ dilemma another way: “How do you denounce the Nusra Front as extremists when they are playing such an important military role and when they look disciplined, resourceful and committed?”
From the start, the Syrian government has sought to portray the rebels as terrorists carrying out an international plot to weaken the country, and the rise of extremist groups has strengthened its case and increased support among Syrians who fear that a rebel victory could mean the end of the secular Syrian state.
Many rebels and opposition activists complain about the Western focus on Islamist groups, some even dismissing the opposition’s ideological differences.
“We all want an Islamic state and we want Shariah to be applied,” said Maawiya Hassan Agha, a rebel activist reached by Skype in the northern village of Sarmeen. He said a country’s laws should flow from its people’s beliefs and compared Syrians calling for Islamic law with the French banning Muslim women from wearing face veils.
“In France, people don’t like face veils so they passed laws against them,” he said. “It’s the same thing here. It’s our right to push for the laws we want.”
An employee of The New York Times contributed reporting from Aleppo, Syria.
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