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...