Three years after the CIA began secretly shipping lethal aid to rebels fighting against Syrian President Bashar al-Assad, battlefield losses and fears that a Donald Trump administration will abandon them have left tens of thousands of opposition fighters weighing their alternatives.

Among the options, say U.S. officials, regional experts and the rebels themselves, are a closer alliance with better-armed al-Qaeda and other extremist groups, receipt of more sophisticated weaponry from Sunni states in the Persian Gulf region opposed to a U.S. pullback, and adoption of more traditional guerrilla tactics, including sniper and other small-scale attacks on both Syrian and Russian targets.

Just over a year ago, the opposition held significant territory inside Syria. Since then, in the absence of effective international pushback, Russian and Syrian airstrikes have relentlessly bombarded their positions and the civilians alongside them. On the ground, Syrian government troops — bolstered by Iran, Lebanon’s Hezbollah, and Shiite militia forces from Iraq — have retaken much of that ground.

In brutal attacks over the past three weeks, they have been driven out of much of the eastern Aleppo stronghold that they have occupied since 2012.

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Trump has made clear that his priority in Syria is the separate fight against the Islamic State, ideally in cooperation with Russia and the Syrian government, as well as other allies. While still vague about his plans, the president-elect has rejected the Obama administration’s view that ending the civil war and bringing Assad to the negotiating table are ultimately key to victory over the Islamic militants, and indicated he will curtail support for the opposition.

Trump has repeatedly dismissed the rebels, saying, “We have no idea who these people are.”

“My attitude was you’re fighting Syria, Syria is fighting ISIS, and you have to get rid of ISIS,” he told the Wall Street Journal last month, using another name for the Islamic State.

Assad, in an interview the week after Trump’s election, called the United States a “natural” counterterrorism ally. He has long labeled the opposition as terrorists equal to the Islamic State.

The possibility of cutting loose opposition groups it has vetted, trained and armed would be a jolt to a CIA already unsettled by the low opinion of U.S. intelligence capabilities that Trump had expressed during his presidential campaign.

From a slow and disorganized start, the opposition “accomplished many of the goals the U.S. hoped for,” including their development into a credible fighting force that showed signs of pressuring Assad into negotiations, had Russia not begun bombing and Iran stepped up its presence on the ground, said one of several U.S. officials who discussed the situation on the condition of anonymity because they were not authorized to speak publicly.

The United States estimates that there are 50,000 or more fighters it calls “moderate opposition,” concentrated in the northwest province of Idlib, in Aleppo and in smaller pockets throughout western and southern Syria, and that they are not likely to give up.

“They’ve been fighting for years, and they’ve managed to survive,” the U.S. official said. “Their opposition to Assad is not going to fade away.”

Although their fortunes were boosted last year by U.S. and Saudi Arabia-provided TOW antitank missiles, the rebels have long complained that American assistance has been stingy and has come with too many strings attached. Concerned that more sophisticated weapons, including portable antiaircraft missiles, would end up in the hands of extremists, President Obama refused to send them and prevailed upon regional allies to impose similar restrictions on their own arms shipments.

Now, said one U.S.-vetted rebel commander, “we are very frustrated. The United States refuses to provide weapons we need, and yet it still thinks it can tell us what to do. They promise support and then watch us drown.”

“America will have no influence if our comrades are forced [to retreat to] Idlib” from Aleppo, said the commander, who asked not to be identified to speak about sensitive rebel relations with the United States.

Most rebels already forced to relinquish territory have gone to Idlib, which is fast becoming a holding pen for what is left of the rebellion. The area is dominated by as many as 10,000 fighters for Jabhat al-Nusra, the al-Qaeda-linked group now known as Jabhat Fatah al-Sham, and an equal number of Ahrar al-Sham, an Islamist group tied to the wider rebel movement that the United States does not consider terrorist.

Some experts, including Trump’s designated White House national security adviser, retired Lt. Gen. Michael Flynn, think that the growing operational alliance between the rebels and extremist groups began long ago.

Flynn argued last year that Obama’s Syria strategy of first withholding, then offering only measured support for the opposition through a covert CIA program, effectively allowed extremist organizations to grow at rebel expense. Asked in a July 2015 al Jazeera interview whether there should have been stronger early support for the opposition, Flynn said: “When you don’t get in and help somebody, they’re going to find other means to achieve their goals. . . . We should have done more earlier on in this effort.”

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At the same time, Flynn has said, the administration played down early intelligence indicating that al-Nusra and eventually the Islamic State organization, which combined Islamist extremists and former Iraqi army officers left adrift by the 2003 U.S. invasion, were growing rapidly.

In a book published last summer, Flynn wrote that they are allied with those who “share their hatred of the West,” including “North Korea, Russia, China, Cuba and Venezuela.”

But in an analysis looking forward, echoed by Trump and certain to be influential in the incoming White House, Flynn has also outlined a World War II -type global alliance, including both the United States and Russia, under a single leadership, to combat what he has called “Islam’s . . . political ideology.”

Others have noted that cutting off the opposition would not only support Russian and Syrian aims but also would benefit Iran at the perceived expense of Saudi Arabia, Qatar and other regional U.S. allies who view that country as an existential threat.

“There will be significant reputational costs with our allies in the region if we abandon support of the moderate opposition,” said Rep. Adam B. Schiff (Calif.), the ranking Democrat on the House Intelligence Committee.

He said the question is “whether our Gulf allies can count on us or they can’t, whether the Iranians are going to be given free rein or they won’t.”

“A lot obviously will depend on what the president-elect does, what his advisers urge him to do,” Schiff said. Referring to retired Marine Gen. James Mattis, Trump’s choice for defense secretary, Schiff added, “I think Gen. Mattis will have different views . . . [that] recognize the implications in terms of Iranian influence in the region.”

Disagreement over whether to take a tougher line against Russia in Syria — including direct military intervention on behalf of civilians and, indirectly, the rebels — in Aleppo and beyond has already caused deep divisions between Obama’s State Department and the reluctant Defense Department and the White House.

Secretary of State John F. Kerry has continued negotiations over a cease-fire, meeting again with Russian Foreign Minister Sergei Lavrov in Rome on Friday. Talks have focused on an agreement to safely deliver humanitarian aid and to evacuate both civilians, who want to leave, and the al-Nusra forces that Russia says are the majority of some several thousand anti-Assad fighters in the eastern part of the city. U.S. officials think the militants there number in the hundreds.

But Kerry has had little leverage to persuade Moscow to change its strategy, designed to ensure a military victory for Assad.

As the incoming Trump administration considers withdrawing from involvement in either assisting or resolving the civil war, others have indicated they will move into the anticipated vacuum.

Qatar has said it will continue supporting and supplying the rebels, regardless of what the United States decides.

“We want to have the U.S. with us, for sure. They have been our historic ally,” Qatar Foreign Minister Mohammed bin Abdulrahman Jassim al-Thani said last week in an interview with Reuters in Doha. “But if they want to change their minds . . . we are not going to change our position.”

Loveluck reported from Beirut.

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