The Obama administration dispatched dozens of troops into Chad to chase down Boko Haram this week, attempting to rescue more than 200 girls abducted from an al-Qaeda affiliate that the administration resisted adding to the list of foreign terrorist organizations for years. The resistance to adding this group to the State Department FTO list came from a mindset that insisted that AQ was on the run and that radical Islamist terrorism was not a direct threat to the US. Even the terrorist attack on the Benghazi consulate got blamed initially on local outrage over a YouTube video rather than the predictable culmination of an escalating series of attacks on Western interests by the Islamist terror networks that Western intervention had freed from Moammar Qaddafi’s anti-terrorism efforts.

The White House and the US intel community is on a collision course about the assessment of AQ, Eli Lake reported yesterday for The Daily Beast, and US security policy is in the crosshairs:

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.

What about Afghanistan? While campaigning for president in 2007-8, Obama blasted the Bush administration for taking on Iraq while the fight in Afghanistan languished. Once in office, Obama increased troop strength (after a long delay, and only with a timetable for draw-down), and not long after declared al-Qaeda vanquished in Afghanistan. The administration has repeatedly asserted that fewer than 100 AQ assets remain in the country, but intel sources tell Lake that this claim is long out of date. Since the drawdown, AQ has returned with a vengeance:

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?”

Lake brings us back around to Boko Haram. When US special forces killed Osama bin Laden in May 2011, they captured a treasure trove of communications that showed just how virulent the AQ network had become. Among that trove, these sources claim, were communications that showed in 2011 the direct connection between AQ and Boko Haram:

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.

If true, that puts the decision to keep Boko Haram off the FTO list — and off the US counterterrorism radar — in an entirely new light. It appears at this time — and strongly, in the case of Benghazi — that the Obama administration wanted to believe AQ and its affiliates posed no threat and closed their minds to all evidence to the contrary, and so ignored real threats until far too late.

Not surprisingly, then, Obama’s finding it difficult to get any traction for further retreat:

In an ambitious address delivered a year ago Friday at the National Defense University, Obama said that the core of al-Qaeda was “on the path to defeat” and that the upcoming end of the war in Afghanistan had brought America to a “crossroads.”

But many of the changes Obama outlined have proved easier said than done, including new rules governing the use of force abroad, increased public information on and congressional oversight of lethal attacks with drones, and efforts to move the CIA out of the killing business.

Some initiatives have become mired in internal debates, while others have taken a back seat to other pressing issues and perceived new terrorism dangers. Congress, while demanding faster change in some areas, has resisted movement in others.

In a Senate hearing Wednesday, irate lawmakers criticized senior administration officials over the lack of follow-up with one of the strategy’s principal goals: Obama had said he was looking forward to “engaging Congress and the American people in efforts to refine and ultimately repeal” the nearly 13-year-old congressional authorization to use force against those individuals, groups and nations responsible for the 9/11 attacks.

Since then, “he has been silent and done nothing,” said Sen. Bob Corker (Tenn.), the senior Republican on the Foreign Relations Committee.

Perhaps we should see more of the documents and more of the actual threat assessments before proceeding down this path.