On Feb. 22, 2006, the Askaria shrine in Samarra, nicknamed the Golden Mosque for its glistening dome and one of Shiism’s holiest sites, was destroyed by bombs planted by the Al Qaeda in Iraq terrorist organization. In response, furious Shiites began organizing militias, who then embarked on a systematic, cold-blooded sectarian killing spree through Sunni neighborhoods, who organized similar militias in self-defense. If Lt. Gen. Stanley McChrystal, commander of Joint Special Operations Command (JSOC), couldn’t find and eliminate Abu Musab al-Zarqawi and his network, the likelihood of Iraq plunging into all-out sectarian war would become a frightening reality.

Not long after he became JSOC commander in 2003, McChrystal recognized that the traditional compartmentalization between the services and agencies tasked with the gathering of counter-terrorism intelligence was counter-productive. In Iraq’s rapidly changing environment, such bureaucratic turf protecting had to be changed. As McChrystal wrote in his memoir, My Share of the Task, “It required turning a hierarchical force with stubborn habits of insularity into one whose success relied on reflexive sharing of information and a pace of operations that could feel more frenetic than deliberate.” In short, he took a chapter from the terrorists’ handbook and create a counter-terrorist network as nimble and as opportunistic and the quarry he was hunting.

In July 2004 JSOC set up a secure intelligence center at a former Iraqi air base in Balad, about fifty miles north of Baghdad. There JSOC requisitioned a hangar and instead of installing a warren of cubicles, only a few offices were created along the hangar’s walls. Work was done out in the open on long tables within the hangar’s cavernous enclosure, and the free flow of information was encouraged between those cleared to work there. At the same time, field operations were restructured to make rapid response a top priority.

The breakthrough in the hunt for al-Zarqawi came on May 18, 2006. An interrogation report of a detainee contained detailed information about Zarqawi’s spiritual advisor, Shiekh Abd al-Rahman, including his Baghdad address, and that he regularly visited Zarqawi every seven to ten days.

An around-the-clock watch of Rahman’s home by reconnaissance drones was instituted and every aspect of his movements tracked and recorded. As days became weeks, pressure began building to make a move on Rahman.

On the morning of June 7, 2006, an operator observed al-Rahman’s car on a major highway heading north out of Baghdad. At one point the car pulled off to the side of the road. Al-Rahman exited and transferred to an approaching truck. Alerts went out to other members of the team. At Baqubah, al-Rahman transferred to a white pickup with a red stripe that drove him to a box-like two-story house near the town of Hibhib. Shortly after 5 p.m. an operator watching the video feed from a drone called out. A heavyset man dressed in black was observed checking traffic on the frontage road before returning to the house.

“That’s [al-Zarqawi],” McChrystal said. When a ground assault was judged not feasible, the decision was made to have F-16s bomb the house. A special operations team would land immediately afterword to retrieve the bodies and gather intelligence.

With time now of the essence, things threatened to spin out of control. The engines on one of the mission’s two Air Force Special Operations Command (AFSOC) helicopters refused to start. A replacement wouldn’t arrive for thirty minutes. The working helicopter was ordered airborne, the second to follow as soon as it could. Then when the JTAC relayed the strike order to two F-16s in the area, only one was available. The other was conducting a mid-flight refueling. The lone F-16 was ordered in.

“You are cleared to engage.”

—JSOC Joint Terminal Attack Controller (JTAC) message to F-16 pilot over Hibhib, June 7, 2006

In its first pass over the target, the F-16 simply flew over the house. The order had been improperly worded; the pilot had not dropped his bombs. The change was made, and on the second pass, the target was destroyed.

The special operations ground team arrived as Iraqi police were putting a body into an ambulance. The team took control of the ambulance and retrieved the mortally wounded al-Zarqawi, who died a few minutes later. His body and that of Abd al-Rahman were airlifted back to JSOC headquarters.

On June 8, Iraqi Prime Minister Nouri al-Maliki held a press conference announcing al-Zarqawi’s death. Coalition commander Gen. George Casey noted, “Although the designated leader of Al Qaeda in Iraq is now dead, the terrorist organization still poses a threat.” The words were prophetic, for the summer of 2006 would see a rise in Iraqi bloodshed. But with Al Qaeda in Iraq’s charismatic leader gone, eventually, the killing began to recede.