Over the summer, as ISIS fighters were winning swaths of territory in Iraq, U.S. intelligence agencies were also focused on the group’s ostensible jihadist rivals in neighboring Syria.

American analysts had pieced together detailed information on a pending attack from an outfit that informally called itself “the Khorasan Group” to use hard-to-detect explosives on American and European airliners.

As the Khorasan Group came closer to executing the attack, however, U.S. intelligence agencies lost track of the plotters. “We had some information on their plans that did not pan out over the summer,” one senior U.S. intelligence official told The Daily Beast. “They shut it down and went dark.”

Since 2012, the U.S. intelligence community has tracked the movement of several senior al Qaeda planners into Syria, where they have set up operations aimed not at Bashar al-Assad’s regime, like many of their fellow militants. Instead, these planners were focused on Europe and America. At first, the group was believed by U.S. intelligence agencies to be al Qaeda’s senior operatives and linked to al Qaeda’s franchise in Syria known as al-Nusra. But beginning in the spring, the intelligence community began to call the outfit “the Khorasan Group,” named in part because many of its members are affiliated with the Khorasan Shura, a leadership council within al Qaeda. Khorasan in Jihadist literature refers to the region that includes Pakistan, Afghanistan, and Iran.

“My suspicion is what we are hearing about Khorasan is only part of the group,” said Daveed Gartenstein-Ross, an expert on al Qaeda at the Foundation for the Defense of Democracies. “It strikes me as quite possible we are only hearing about the external operations wing and not the entire organization.”

Last week Director of National Intelligence James Clapper became the first senior government official to publicly name the Khorasan Group at an intelligence conference in Washington. The Associated Press published the first major story on the organization on September 13. On Tuesday, U.S. military leaders and President Obama himself publicly named the Khorasan Group as one of the targets of the airstrikes Monday evening and Tuesday morning inside Syria.

Jihadist media claimed two of the group’s leaders, Muhsin al-Fadhli and Abu Yousef al-Turki, were killed in the attack. A Pentagon spokesman said he could not confirm those reports.

The attack on the Khorasan Group, which consists of senior al Qaeda operatives loyal to the group’s central leadership, presents an unusual dilemma for Obama’s own war planners. Currently al Qaeda’s official franchise in Syria, al-Nusra, is fighting with ISIS, the breakaway Jihadist group whose positions were bombed in Raqqa, Syria, in the same flurry of U.S. airstrikes Monday night and Tuesday morning.

Perhaps striking two sides in Syria’s four-sided (or more) civil war will strengthen America’s new allies, the moderate rebels in the long run. (In the short term, it may not mean much.) But the attacks could also weaken the most potent opponents to the dictator Bashar al-Assad. Or, perhaps worse still, the U.S. strikes could drive ISIS and al Qaeda back together, creating a jihadist Frankenstein.

U.S. intelligence officials have privately and publicly described al Qaeda’s relationship with ISIS as a competitive one, with both groups staking claim to the leadership of the global jihadist movement. “It’s no secret al Qaeda is in a huge competition with the Islamic State,” Gartenstein-Ross said, noting that a spectacular terrorist attack on a Western target is one way for al Qaeda to make inroads against ISIS. "What’s been going on is al Qaeda exercising a strategy to compete with them. And it seems like the Khorasan Group is a part of that.”

U.S. officials confirm to The Daily Beast that over the summer, the U.S. intelligence community began closely tracking a plot to sneak non-metallic bombs inside European and American airliners. On Tuesday, Army Lt. Gen. William C. Mayville Jr., director of operations for the Joint Chiefs of Staff, said the Khorasan Group was in the execution phase of a plot against the West.

An attack involving multiple airliners is much more sophisticated and deadly than what U.S. counter-terrorism analysts believe ISIS is capable of launching inside the United States. For now, ISIS’s strength is in seizing territory in the Middle East, not in attacking Middle America. The threat from ISIS is largely based on its ability to inspire and radicalize Westerners to launch fairly simple attacks inside Europe and America similar to the bombing at the Boston Marathon in 2013. The planning from the Khorasan Group, though, suggests at least an aspiration to launch more-coordinated and larger attacks on the West in the style of the 9/11 attacks from 2001.

The Khorasan Group has been experimenting with different types of non-metallic explosives for attacks on Western targets, according to U.S. intelligence officials. Most of the members of the group come from Yemen, Afghanistan, or Pakistan and have for months been coordinating with bomb-makers drawn from al Qaeda’s affiliate in the Arabian Peninsula, the most persistent and creative of al Qaeda groups in efforts to bomb U.S.-bound passenger jets.

ISIS and al Qaeda bitterly split earlier this year, and have since attacked one another on occasions. But some analysts now fear that striking at ISIS and al Qaeda could persuade the two groups to put aside their sharp differences and come together. Indeed, jihadist ideologues loyal to both warring factions have had similar messages for their followers in the wake of the airstrikes.

For example, prominent ISIS supporter Shaibat Al-Hamad called on jihadists in Qatar and the United Arab Emirates to kill any Westerners in their countries, according to the Middle East Media Research Institute, a U.S.-based nonprofit that tracks online jihadi activity. That’s a move more reminiscent of al Qaeda than of ISIS.

The influential jihadist ideologue Abu Muhammad Al-Maqdisi, who has in the past denounced ISIS as deviant and has urged the group to release British hostage Alan Henning because aid workers shouldn’t be harmed, has told his supporters that “Muslims must not support Crusader aggression against” ISIS.

An easing of tensions between al Qaeda and ISIS presents dangers for America in its military campaign in the Levant. It could persuade hardline Islamist brigades, the largest of the insurgent militias among the Syrian rebels, to oppose the West and to halt their own war against ISIS. “There is a major risk here,” says a European intelligence source. “Al-Nusra has lot of influence among the Islamists—they have been allies together not only when it comes to fighting Assad but also in battling ISIS. If al-Nusra forms an alliance with ISIS, some of them will too.”

The attacks on the Khorasan Group also complicate U.S. efforts to partner with the more moderate opposition. One Syrian rebel group supported in the past by the United States condemned the airstrikes on Tuesday. Harakat Hazm, a rebel group that received a shipment of U.S. anti-tank weapons in the spring, called the airstrikes “an attack on national sovereignty” and charged that foreign-led attacks only strengthen the Assad regime. The statement comes from a document, purportedly from the group, that has circulated online and was posted in English translation from a Twitter account called Syria Conflict Monitor. Several Syria experts, including the Brookings Doha Center’s Charles Lister, believe the document to be authentic.

Before the official statement, there were signs that Harakat Hazm was making alliances in Syria that could conflict with its role as a U.S. partner. In early Septemeber a Harakat Hazm official told a reporter for the L.A. Times: “Inside Syria, we became labeled as secularists and feared Nusra Front was going to battle us…But Nusra doesn't fight us, we actually fight alongside them. We like Nusra.”

The initial round of U.S. and allied airstrikes inside Syria were also not coordinated with Free Syrian Army brigades on the ground, opposition leaders told The Daily Beast. The leadership of the Syrian National Coalition was notified over the weekend that the airstrikes would begin, but there was no operational coordination and Free Syrian Army brigades were not used as spotters and were not given specific information that would have allowed them to capitalize on the strikes by moving into areas where ISIS was hit.

“These strikes were done with U.S. and allied information, not with information from the FSA. That doesn’t mean that later on there won’t be coordinated air operations sometime in the future,” said one opposition leader. “We heard the Pentagon say this is just the beginning. And there is expectation for close coordination going forward.”

FSA brigades near Aleppo have received increased deliveries of light weapons, ammunition, and even some anti-tank missiles recently, the official said. But those weapons were meant to enable FSA brigades in the northern Aleppo suburbs to defend their positions against ongoing ISIS assaults.

“Airstrikes against ISIS inside Syria will not be helpful. Airstrikes will not get rid of ISIS. Airstrikes are like just tickling ISIS,” Hussam Al Marie, the spokesman for the FSA in northern Syria, told The Daily Beast last month. At the time, he had no comment about another jihadist group whose name had only begun to pass Western lips.

—with additional reporting by Jamie Dettmer, Josh Rogin, and Jacob Siegel