In 2012, the Obama administration produced a draft National Intelligence Estimate that reached a surprising conclusion: al Qaeda was no longer a direct threat to America. That classified assessment, which has never before been publicly disclosed, was in keeping with the message coming from the White House. President Obama rode to re-election in 2012 partly on the success of the raid that killed Osama bin Laden. At rallies and in press conferences, the president and top officials publicly said al Qaeda was on the run.

But some senior U.S. intelligence officials, like Defense Intelligence Agency Director Gen. Michael Flynn, fought hard against that assessment, which amounted to an official pronouncement of the American intelligence community’s collected wisdom. Flynn and his faction won a partial victory, striking the judgment that the terrorist group no longer posed a threat to the homeland. “Flynn and others at the time made it clear they would not go along with that kind of assessment,” one U.S. intelligence officer who worked on the al Qaeda file told The Daily Beast. “It was basically: ‘Over my dead body.’”

Since that internal clash—and since Obama said in his 2012 State of the Union that “al Qaeda operatives who remain are scrambling, knowing that they can’t escape the reach of the United States of America”—the terror group has thrived throughout the Islamic world. In the last year alone, al Qaeda has established safe havens in Libya, Syria and Iraq.

And so naturally, the White House has softened its earlier position, concluding that al Qaeda and its affiliates still represented a serious threat. But the tension between the White House and many top military and intelligence officials fighting the long war remain.

In interviews with many of them, a common theme is sounded: The threat from al Qaeda is rising, but the White House is looking to ratchet down the war against these Islamic extremists. As a result, intelligence gathered on these threats remain shrouded from the public and, in many cases, from senior government officials. And now Congress and the White House are beginning to consider modifying—and possibly revoking—the very authority to find, fix and finish those terrorists who pose the threat today.

One senior U.S. intelligence official told The Daily Beast the frustration was that there is pressure from the White House to downplay the threat from some al Qaeda affiliates. “It comes from the top, it’s the message that al Qaeda is all these small franchise groups and they are not coordinated and threatening,” this official said. “It’s the whole idea of getting us out to place resources against something that they don’t think is a problem. It’s not their war, it’s not our conflict.”

The White House, naturally, has a different position. Caitlin Hayden, the spokeswoman for the National Security Council, in a lengthy email to The Daily Beast outlining White House counter-terrorism policies, said, “As the President has emphasized, we must define our effort not as a boundless ‘global war on terror’ – but rather as a series of persistent, targeted efforts to disrupt, dismantle, and defeat specific networks of violent extremists that threaten the United States.”

And, of course, it should be noted that the U.S. intelligence community still spends an enormous amount of money on counter-terrorism: $17.2 billion in 2013 alone, according to budget documents published by The Washington Post. But that money, after years of unchecked expansion, has leveled off as the nation’s intelligence agencies have begun to steer resources towards cyber security and other issues.

This week, this internal struggle over the response to al Qaeda is reaching a crucial moment. The Senate Foreign Relations Committee on Wednesday will hold a nearly unprecedented hearing on the 2001 law that authorizes a long, global war against al Qaeda and its allies.

At the same time, U.S. intelligence officers say, there is deep division within their ranks–and with the White House—about the strength of al Qaeda in the place where that war began: Afghanistan. The current estimate of the terror group’s presence there says that al Qaeda has a little more than 100 fighters in the country’s province of Kunar. That, these intelligence officers contend, is wildly out of date. “Al Qaeda has a presence all over Afghanistan today,” a senior U.S. intelligence official told The Daily Beast. “This is the conversation that no one wants to have. What are they going to do after 2014 when most of our troops will be gone?”

The frustration isn’t limited to Afghanistan. One of the reasons the 2012 Benghazi attacks still rankle a sizeable segment of the intelligence community is that they see a similar downplaying of the extremist threat in the initial reaction to the strikes. U.S. intelligence officers in Libya on the night of the attacks cabled back that it was a coordinated terrorist attack, only to see Obama administration officials cling to out-of-date talking points that described it as a demonstration gone awry. The Daily Beast has learned that one reason why CIA officers were so quick to conclude the attack was an act of terrorism was because some of the fighters who participated in the attack were being watched by CIA officers at the time on the ground in Libya, according to U.S. intelligence officials and congressional investigators.

Many U.S. al Qaeda experts inside the intelligence community are also critical of the handling of the documents taken from Osama bin Laden’s Pakistani lair. These experts lobbied to declassify many more than the handful that have thus far been released. Some of those documents that were initially slated to be declassified, according to two U.S. intelligence officials, were letters between leaders of Boko Haram and bin Laden. In other words, they showed that the Nigerian terror group, now infamous for its mass kidnappings, was tied to al Qaeda’s leader. Those records are still being kept under wraps. Rep. Devin Nunes, a Republican on the House Permanent Select Committee on Intelligence, has openly called on the Obama administration to declassify all of the documents.

In all of these examples, the common theme of frustration is that while the political will to fight a long war against a less centralized al Qaeda network wanes in America, the threat gathers overseas. “There is a desire for peace and I understand that. Everyone admits theoretically that the enemy gets a vote. But the war is not over till the enemy says it’s over,” James Mattis, who served as Obama’s commander of Central Command between 2010 and 2013, told The Daily Beast. “There is some disagreement or reservations about whether people are trying to wish things away on a timetable.”

Mattis is not alone in this view. Sen. Dianne Feinstein, the Democratic chairwoman of the Senate Select Committee on Intelligence, told CNN on Sunday, “Terror is not down in the world. It is up, both deaths, injuries, in many, many different places. Al Qaeda has metastasized. The question becomes how do we prevent an attack in this country.” James Comey, the FBI director, said in an interview with The New York Times that he underestimated the threat from al Qaeda when he came into the job nine months ago.

These days the rhetoric from the Obama administration about al Qaeda being on the run is largely gone. Publicly and privately Obama has acknowledged that the threat of jihadists has metastasized. In this year’s state of the union Obama expressed the view as: “While we have put al Qaeda’s core leadership on a path to defeat, the threat has evolved, as al Qaeda affiliates and other extremists take root in different parts of the world.” But those lines were delivered in a speech that promised to get America off of a “permanent war footing” and expressing skepticism that the lethal combination of unmanned drones and electronic eavesdropping alone can defeat terrorism.

Tommy Vietor, who served as the spokesman for the National Security Council in Obama’s first term, recalled a meeting he attended with Obama on the crisis in Mali. He said the president understood the threat from al Qaeda’s core leadership had diminished, while the threat of affiliates had grown stronger. At the end of the meeting though, he said the president remarked, “What will be required for a crisis like that is not a drone-based program dotting the continent. It will be a sustained political process that includes economic development.”

It’s an irony for Obama, who has been attacked by progressives for relying too heavily on drone attacks in his war on terrorism. But Vietor and many other U.S. intelligence and military officials also point out the president has had to balance priorities and limited resources. And there are those within the intelligence community who share that view—who worry that an obsessive focus on al Qaeda distracted the United States from other adversaries, like Russia and China.

“I think part of the difference is some of the members of the military and the intelligence community understandably see a matrix in the morning of unbelievable threats. They do everything they can to prevent those threats from materializing and they would like as much resources as they can get to do that,” Vietor told The Daily Beast. “The president wakes up in the morning, he sees that same matrix, for a long time he also saw a briefing of threats to the world economy that is arguably as scary. And he has to do deal with all of them. That means making tough choices and seeing the whole playing field, not just a day at a time, but a decade at a time.”

Obama may have his chance to take America off of a war footing. The hearing Wednesday on the Authorization for the Use of Military Force is being held at the behest of Sen. Bob Corker, the Republican ranking member on the committee who is often positioned between his own parties hawks like Sen. John McCain on foreign policy and war-on-terror skeptics like Sen. Rand Paul.

Corker last year in a hearing on the AUMF said it was difficult to tie the groups targeted by the U.S. military and intelligence community today to the organization that attacked the United States on 9/11. “Congress should amend the law to specify exactly how and when the president can use drones and kill or capture missions to kill people,” he said at the time.

Hayden said the White House was open to modifying the AUMF. “We will engage further with Congress and the American people on efforts to ensure that the legal authorities for our counterterrorism and detention operations are appropriately tailored,” she said.

But it will be difficult to “appropriately tailor” the authorities and operations that comprise the war on terror if so many of the analysts and officers on the front lines believe the threat from the group is rising.

Or, as one senior U.S. intelligence official told The Daily Beast: “Take this ‘al Qaeda is on the run’ message, it’s something you’ve seen in the last couple of years. If they are on the run, they are on the run to the United States.”