President Obama has ordered the Pentagon to find and kill the leaders of an al-Qaeda-linked group in Syria that the administration had largely ignored until now and that has been at the vanguard of the fight against the Syrian government, U.S. officials said.
The decision to deploy more drones and intelligence assets against the militant group formerly known as Jabhat al-Nusra reflects Obama’s concern that it is turning parts of Syria into a new base of operations for al-Qaeda on Europe’s southern doorstep, the officials said.
The move underlines the extent to which Obama has come to prioritize the counter­terrorism mission in Syria over efforts to pressure President Bashar al-Assad to step aside, as al-Nusra is among the most effective forces­­ battling the Syrian government.
That shift is likely to accelerate once President-elect Donald Trump takes office. Trump has said he will be even more aggressive in going after militants than Obama, a stance that could lead to the expansion of the campaign against al-Nusra, possibly in direct cooperation with Moscow. The group now calls itself Jabhat Fatah al-Sham — or Front for the Conquest of Syria — and says it has broken with al-Qaeda, an assertion discounted by U.S. officials.
The United States has conducted sporadic strikes in the past against veteran al-Qaeda members who migrated to northwestern Syria from Afghanistan and Pakistan to join al-Nusra and whom U.S. officials suspected of plotting against the United States and its allies.
Obama’s new order gives the U.S. military’s Joint Special ­Operations Command, or JSOC, wider authority and additional intelligence-collection re­sources to go after al-Nusra’s broader leadership, not just al-Qaeda veterans or those directly involved in external plotting.
The White House and State Department led the charge within the Obama administration for prioritizing action against the group. Pentagon leaders were reluctant at first to pull resources away from the fight against the Islamic State.

But aides say Obama grew frustrated that more wasn’t being done by the Pentagon and the intelligence community to kill al-Nusra leaders given the warnings he had received from top counter­terrorism officials about the gathering threat they posed.
In the president’s Daily Brief, the most highly classified intelligence report produced by U.S. spy agencies, Obama was repeatedly told over the summer that the group was allowing al-Qaeda leaders in Pakistan and Afghanistan to create in northwest Syria the largest haven for the network since it was scattered after the Sept. 11, 2001, attacks. Officials also warned Obama that al-Nusra could try to fill the void as its rival, the Islamic State, lost ground.
Lisa Monaco, Obama’s White House homeland security and counter­terrorism adviser, said Obama’s decision “prioritized our fight against al-Qaeda in Syria, including through targeting their leaders and operatives, some of whom are legacy al-Qaeda members.”
“We have made clear to all parties in Syria that we will not allow al-Qaeda to grow its capacity to attack the U.S., our allies, and our interests,” she said in a statement. “We will continue to take action to deny these terrorists any safe haven in Syria.”
To support the expanded push against al-Nusra, the White House pressed the Pentagon to deploy additional armed drones and intelligence-collection assets in the airspace over northwestern Syria, an area that had been sparsely covered by the United States until now because of its proximity to advanced Russian air-defense systems and aircraft.

A bitterly divided Obama administration had tried over the summer to cut a deal with Moscow on a joint U.S.-Russian air campaign against al-Nusra, in exchange for a Russian commitment to ground Syrian government warplanes and to allow more humanitarian supplies into besieged areas. But the negotiations broke down in acrimony, with Moscow accusing the United States of failing to separate al-Nusra from more moderate rebel groups and Washington accusing the Russians of war crimes in Aleppo.
Armed drones controlled by JSOC stepped up operations in September, according to military officials.
Drone strikes by the U.S. military under the program began in October and have so far killed at least four high-value targets, including al-Nusra’s senior external planner. The Pentagon has disclosed two of the strikes so far. One of the most significant strikes — targeting a gathering of al-Nusra leaders on Nov. 2 — has yet to be disclosed, officials said, speaking on the condition of anonymity to discuss operations.
So far, Russian air-defense systems and aircraft haven’t interfered with stepped-up U.S. operations against al-Nusra. Officials attributed Moscow’s acquiescence to the limited number of U.S. aircraft involved in the missions and to Russia’s interest in letting Washington combat one of the Assad regime’s most potent enemies within the insurgency. U.S. officials said they provided notifications to the Russians before the al-Nusra strikes to avoid misunderstandings.
Officials said the expanded al-Nusra campaign was similar to those that Obama has directed against al-Qaeda affiliates in Yemen, Somalia and Pakistan.
While al-Qaeda’s central leadership in Pakistan has been decimated, the United States now faces more threats involving more extremists from more places than at any time since 9/11, Nicholas J. Rasmussen, director of the National Counterterrorism Center, told a Senate committee in September.
The push into the province of Idlib and other parts of northwestern Syria coincides with ­Pentagon-backed offensives in and around Islamic State strongholds in eastern Syria and in Iraq, which have attracted the majority of U.S. military resources and public attention.

White House officials had considered launching a more systematic campaign to destroy al-Nusra from top to bottom, much like the Pentagon’s approach to the Islamic State. But that option was rejected as too resource-intensive. Many of al-Nusra’s fighters are Syrians who joined the group because of its ample supply of weapons and cash, and its commitment to defeating Assad, not to plot against the West.

Officials said the strikes on leadership targets were meant to send a message to more-moderate rebel units, including those backed by the CIA, to distance themselves from the al-Qaeda affiliate. At critical moments during the five-year-old civil war, moderate rebel units have fought alongside al-Nusra in ground operations against Assad’s forces. In fact, U.S. officials credit those rebel campaigns in the spring of 2015 with putting so much pressure on the Syrian government that Russia and Iran decided to double down militarily in support of Assad.
U.S. officials who opposed the decision to go after al-Nusra’s wider leadership warned that the United States would effectively be doing the Assad government's bidding by weakening a group on the front line of the counter- Assad fight. The strikes, these officials warned, could backfire on the United States by bolstering the group’s standing, helping it attract more recruits and resources.
Officials who supported the shift said the Obama administration could no longer tolerate what one of them described as “a deal with the devil,” whereby the United States largely held its fire against al-Nusra because the group was popular with Syrians in rebel-controlled areas and furthered the U.S. goal of putting military pressure on Assad. Russia had accused the United States of sheltering al-Nusra, a charge repeated Thursday in Moscow by Russian Foreign Minister Sergei Lavrov.
“The president doesn’t want this group to be what inherits the country if Assad ever does fall,” a senior U.S. official said. “This cannot be the viable Syrian opposition. It’s al-Qaeda.”
Officials said the administration’s hope is that more-moderate rebel factions will be able to gain ground as both the Islamic State and al-Nusra come under increased military pressure.
A growing number of White House and State Department officials, however, have privately voiced doubts about the wisdom of applying U.S. military power, even covertly, to pressure Assad to step aside, particularly since Russia’s military intervention in Syria last year.
U.S. intelligence officials say they aren’t sure what Trump’s approach to U.S.-backed rebel units will be once he gets briefed on the extent of the covert CIA program. Trump has voiced strong skepticism about arming Syrian rebels in the past, suggesting that U.S. intelligence agencies don’t have enough knowledge about rebel intentions to pick reliable allies.


Defense Secretary Ashton B. Carter and other Pentagon leaders initially resisted the idea of devoting more Pentagon surveillance aircraft and armed drones against al-Nusra. In White House Situation Room meetings, Carter and other top Pentagon officials argued that the military’s resources were needed to combat the Islamic State and that it would be difficult to operate in the airspace given Russia’s military presence, officials said.
While Obama, White House national security adviser Susan E. Rice, Secretary of State John F. Kerry and special presidential envoy Brett McGurk agreed with Carter on the need to keep the focus on the Islamic State, they favored shifting resources to try to prevent al-Nusra from becoming a bigger threat down the road.

A senior defense official said additional drone assets were assigned to the JSOC mission. Carter also made clear that the Pentagon’s goal would be to hit al-Nusra leadership targets, not take strikes to try to separate the moderate rebels from al-Nusra, officials said.
“If we wake up in five years from now, and Islamic State is dead but al-Qaeda in Syria has the equivalent of [the tribal areas of Pakistan] in northwest Syria, then we’ve got a problem,” a second senior U.S. official said.