Jeremy Scahill writes:

Nestled in a back corner of Mogadishu’s Aden Adde International Airport is a sprawling walled compound run by the Central Intelligence Agency. Set on the coast of the Indian Ocean, the facility looks like a small gated community, with more than a dozen buildings behind large protective walls and secured by guard towers at each of its four corners. Adjacent to the compound are eight large metal hangars, and the CIA has its own aircraft at the airport. The site, which airport officials and Somali intelligence sources say was completed four months ago, is guarded by Somali soldiers, but the Americans control access. At the facility, the CIA runs a counterterrorism training program for Somali intelligence agents and operatives aimed at building an indigenous strike force capable of snatch operations and targeted “combat” operations against members of Al Shabab, an Islamic militant group with close ties to Al Qaeda.

As part of its expanding counterterrorism program in Somalia, the CIA also uses a secret prison buried in the basement of Somalia’s National Security Agency (NSA) headquarters, where prisoners suspected of being Shabab members or of having links to the group are held. Some of the prisoners have been snatched off the streets of Kenya and rendered by plane to Mogadishu. While the underground prison is officially run by the Somali NSA, US intelligence personnel pay the salaries of intelligence agents and also directly interrogate prisoners. The existence of both facilities and the CIA role was uncovered by The Nation during an extensive on-the-ground investigation in Mogadishu. Among the sources who provided information for this story are senior Somali intelligence officials; senior members of Somalia’s Transitional Federal Government (TFG); former prisoners held at the underground prison; and several well-connected Somali analysts and militia leaders, some of whom have worked with US agents, including those from the CIA. A US official, who confirmed the existence of both sites, told The Nation, “It makes complete sense to have a strong counterterrorism partnership” with the Somali government.

The CIA presence in Mogadishu is part of Washington’s intensifying counterterrorism focus on Somalia, which includes targeted strikes by US Special Operations forces, drone attacks and expanded surveillance operations. The US agents “are here full time,” a senior Somali intelligence official told me. At times, he said, there are as many as thirty of them in Mogadishu, but he stressed that those working with the Somali NSA do not conduct operations; rather, they advise and train Somali agents. “In this environment, it’s very tricky. They want to help us, but the situation is not allowing them to do [it] however they want. They are not in control of the politics, they are not in control of the security,” he adds. “They are not controlling the environment like Afghanistan and Iraq. In Somalia, the situation is fluid, the situation is changing, personalities changing.”

According to well-connected Somali sources, the CIA is reluctant to deal directly with Somali political leaders, who are regarded by US officials as corrupt and untrustworthy. Instead, the United States has Somali intelligence agents on its payroll. Somali sources with knowledge of the program described the agents as lining up to receive $200 monthly cash payments from Americans. “They support us in a big way financially,” says the senior Somali intelligence official. “They are the largest [funder] by far.”

According to former detainees, the underground prison, which is staffed by Somali guards, consists of a long corridor lined with filthy small cells infested with bedbugs and mosquitoes. One said that when he arrived in February, he saw two white men wearing military boots, combat trousers, gray tucked-in shirts and black sunglasses. The former prisoners described the cells as windowless and the air thick, moist and disgusting. Prisoners, they said, are not allowed outside. Many have developed rashes and scratch themselves incessantly. Some have been detained for a year or more. According to one former prisoner, inmates who had been there for long periods would pace around constantly, while others leaned against walls rocking.