When U.S. Special Operations forces raided several houses in the Iraqi city of Ramadi in March 2006, two Army Rangers were killed when gunfire erupted on the ground floor of one home. A third member of the team was knocked unconscious and shredded by ball bearings when a teenage insurgent detonated a suicide vest.

In a review of the nighttime strike for a relative of one of the dead Rangers, military officials sketched out the sequence of events using small dots to chart the soldiers’ movements. Who, the relative asked, was this man — the one represented by a blue dot and nearly killed by the suicide bomber?

After some hesi­ta­tion, the military briefers answered with three letters: FBI.

The FBI’s transformation from a crime-fighting agency to a counterterrorism organization in the wake of the Sept. 11, 2001, attacks has been well documented. Less widely known has been the bureau’s role in secret operations against al-Qaeda and its affiliates in Iraq and Afghanistan, among other locations around the world.

With the war in Afghanistan ending, FBI officials have become more willing to discuss a little-known alliance between the bureau and the Joint Special Operations Command (JSOC) that allowed agents to participate in hundreds of raids in Iraq and Afghanistan.