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.  The relationship benefited both sides. JSOC used the FBI’s expertise in exploiting digital media and other materials to locate insurgents and detect plots, including any against the United States. The bureau’s agents, in turn, could preserve evidence and maintain a chain of custody should any suspect be transferred to the United States for trial.

The FBI’s presence on the far edge of military operations was not universally embraced, according to current and former officials familiar with the bureau’s role. As agents found themselves in firefights, some in the bureau expressed uneasiness about a domestic law enforcement agency stationing its personnel on battlefields.

FBI’s Hostage Rescue Team (HRT)

The team’s mission was largely domestic, although it did participate in select operations to arrest fugitives overseas, known in FBI slang as a “habeas grab.” In 1987, for instance, along with the CIA, agents lured a man suspected in an airline hijacking to a yacht off the coast of Lebanon and arrested him.  In 1989, a large HRT flew to St. Croix, Virgin Islands, to reestablish order after Hurricane Hugo. That same year, at the military’s request, it briefly deployed to Panama before the U.S. invasion…

After Sept. 11, the bureau took on a more aggressive posture.

In early 2003, two senior FBI counterterrorism officials traveled to Afghanistan to meet with the Joint Special Operations Command’s deputy commander at Bagram air base. The commander wanted agents with experience hunting fugitives and HRT training so they could easily integrate with JSOC forces…Then-Lt. Gen. Stanley A. McChrystal gradually pushed the agency to help the military collect evidence and conduct interviews during raids…In 2005, all of the HRT members in Iraq began to work under JSOC. At one point, up to 12 agents were operating in the country, nearly a tenth of the unit’s shooters..But the FBI’s alliance with JSOC continued to deepen. HRT members didn’t have to get approval to go on raids, and FBI agents saw combat night after night in the hunt for targets…

FBI-JSOC operations continue in other parts of the world. When Navy SEALs raided a yacht in the Gulf of Aden that Somali pirates had hijacked in 2011, an HRT agent followed behind them. After a brief shootout, the SEALs managed to take control of the yacht.  Two years later, in October 2013, an FBI agent with the HRT was with the SEALs when they stormed a beachfront compound in Somalia in pursuit of a suspect in the Nairobi mall attack that had killed dozens.  That same weekend, U.S. commandos sneaked into Tripoli, Libya, and apprehended a suspected al-Qaeda terrorist named Nazih Abdul-Hamed al-Ruqai as he returned home in his car after morning prayers. He was whisked to a Navy ship in the Mediterranean and eventually to New York City for prosecution in federal court.  Word quickly leaked that Delta Force had conducted the operation. But the six Delta operators had help. Two FBI agents were part of the team that morning on the streets of Tripoli.

Adam Goldman and Julie Tate, Inside the FBI’s secret relationship with the military’s special operations, The Washington Post, Apr. 10, 2014