Gutteridge, who has worked extensively tracking the disappearances of terror suspects in Kenya, was deported from Kenya on May 11.

The underground prison where Hassan is allegedly being held is housed in the same building once occupied by Somalia’s infamous National Security Service (NSS) during the military regime of Siad Barre, who ruled from 1969 to 1991. The former prisoner who met Hassan there said he saw an old NSS sign outside. During Barre’s regime, the notorious basement prison and interrogation center, which sits behind the presidential palace in Mogadishu, was a staple of the state’s apparatus of repression. It was referred to as Godka, “The Hole.”

“The bunker is there, and that’s where the intelligence agency does interrogate people,” says Abdirahman “Aynte” Ali, a Somali analyst who has researched the Shabab and Somali security forces. “When CIA and other intelligence agencies—who actually are in Mogadishu—want to interrogate those people, they usually just do that.” Somali officials “start the interrogation, but then foreign intelligence agencies eventually do their own interrogation as well, the Americans and the French.” The US official said that US agents’ “debriefing” prisoners in the facility has “been done on only rare occasions” and always jointly with Somali agents.

Some prisoners, like Hassan, were allegedly rendered from Nairobi, while in other cases, according to Aynte, “the US and other intelligence agencies have notified the Somali intelligence agency that some people, some suspects, people who have been in contact with the leadership of Al Shabab, are on their way to Mogadishu on a [commercial] plane, and to essentially be at the airport for those people. Catch them, interrogate them.”

* * *

In the eighteen years since the infamous “Black Hawk Down” incident in Mogadishu, US policy on Somalia has been marked by neglect, miscalculation and failed attempts to use warlords to build indigenous counterterrorism capacity, many of which have backfired dramatically. At times, largely because of abuses committed by Somali militias the CIA has supported, US policy has strengthened the hand of the very groups it purports to oppose and inadvertently aided the rise of militant groups, including the Shabab. Many Somalis viewed the Islamic movement known as the Islamic Courts Union, which defeated the CIA’s warlords in Mogadishu in 2006, as a stabilizing, albeit ruthless, force. The ICU was dismantled in a US-backed Ethiopian invasion in 2007. Over the years, a series of weak Somali administrations have been recognized by the United States and other powers as Somalia’s legitimate government. Ironically, its current president is a former leader of the ICU.

Today, Somali government forces control roughly thirty square miles of territory in Mogadishu thanks in large part to the US-funded and -armed 9,000-member AMISOM force. Much of the rest of the city is under the control of the Shabab or warlords. Outgunned, the Shabab has increasingly relied on the linchpins of asymmetric warfare—suicide bombings, roadside bombs and targeted assassinations. The militant group has repeatedly shown that it can strike deep in the heart of its enemies’ territory. On June 9, in one of its most spectacular suicide attacks to date, the Shabab assassinated the Somali government’s minister of interior affairs and national security, Abdishakur Sheikh Hassan Farah, who was attacked in his residence by his niece. The girl, whom the minister was putting through university, blew herself up and fatally wounded her uncle. He died hours later in the hospital. Farah was the fifth Somali minister killed by the Shabab in the past two years and the seventeenth official assassinated since 2006. Among the suicide bombers the Shabab has deployed were at least three US citizens of Somali descent; at least seven other Americans have died fighting alongside the Shabab, a fact that has not gone unnoticed in Washington or Mogadishu.

During his confirmation hearings in June to become the head of the US Special Operations Command, Vice Admiral William McRaven said, “From my standpoint as a former JSOC commander, I can tell you we were looking very hard” at Somalia. McRaven said that in order to expand successful “kinetic strikes” there, the United States will have to increase its use of drones as well as on-the-ground intelligence, surveillance and reconnaissance operations. “Any expansion of manpower is going to have to come with a commensurate expansion of the enablers,” McRaven declared. The expanding US counterterrorism program in Mogadishu appears to be part of that effort.

In an interview with The Nation in Mogadishu, Abdulkadir Moallin Noor, the minister of state for the presidency, confirmed that US agents “are working with our intelligence” and “giving them training.” Regarding the US counterterrorism effort, Noor said bluntly, “We need more; otherwise, the terrorists will take over the country.”

It is unclear how much control, if any, Somalia’s internationally recognized president, Sheikh Sharif Sheikh Ahmed, has over this counterterrorism force or if he is even fully briefed on its operations. The CIA personnel and other US intelligence agents “do not bother to be in touch with the political leadership of the country. And that says a lot about the intentions,” says Aynte. “Essentially, the CIA seems to be operating, doing the foreign policy of the United States. You should have had State Department people doing foreign policy, but the CIA seems to be doing it across the country.”

While the Somali officials interviewed for this story said the CIA is the lead US agency on the Mogadishu counterterrorism program, they also indicated that US military intelligence agents are at times involved. When asked if they are from JSOC or the Defense Intelligence Agency, the senior Somali intelligence official responded, “We don’t know. They don’t tell us.”

In April Ahmed Abdulkadir Warsame, a Somali man the United States alleged had links to the Shabab, was captured by JSOC forces in the Gulf of Aden. He was held incommunicado on a US Navy vessel for more than two months; in July he was transferred to New York and indicted on terrorism charges. Warsame’s case ignited a legal debate over the Obama administration’s policies on capturing and detaining terror suspects, particularly in light of the widening counterterrorism campaigns in Somalia and Yemen.

On June 23 the United States reportedly carried out a drone strike against alleged Shabab members near Kismayo, 300 miles from the Somali capital. As with the Nabhan operation, a JSOC team swooped in on helicopters and reportedly snatched the bodies of those killed and wounded. The men were taken to an undisclosed location. On July 6 three more US strikes reportedly targeted Shabab training camps in the same area. Somali analysts warned that if the US bombings cause civilian deaths, as they have in the past, they could increase support for the Shabab. Asked in an interview with The Nation in Mogadishu if US drone strikes strengthen or weaken his government, President Sharif replied, “Both at the same time. For our sovereignty, it’s not good to attack a sovereign country. That’s the negative part. The positive part is you’re targeting individuals who are criminals.”

A week after the June 23 strike, President Obama’s chief counterterrorism adviser, John Brennan, described an emerging US strategy that would focus not on “deploying large armies abroad but delivering targeted, surgical pressure to the groups that threaten us.” Brennan singled out the Shabab, saying, “From the territory it controls in Somalia, Al Shabab continues to call for strikes against the United States,” adding, “We cannot and we will not let down our guard. We will continue to pummel Al Qaeda and its ilk.”

While the United States appears to be ratcheting up both its rhetoric and its drone strikes against the Shabab, it has thus far been able to strike only in rural areas outside Mogadishu. These operations have been isolated and infrequent, and Somali analysts say they have failed to disrupt the Shabab’s core leadership, particularly in Mogadishu.

In a series of interviews in Mogadishu, several of the country’s recognized leaders, including President Sharif, called on the US government to quickly and dramatically increase its assistance to the Somali military in the form of training, equipment and weapons. Moreover, they argue that without viable civilian institutions, Somalia will remain ripe for terrorist groups that can further destabilize not only Somalia but the region. “I believe that the US should help the Somalis to establish a government that protects civilians and its people,” Sharif said.

In the battle against the Shabab, the United States does not, in fact, appear to have cast its lot with the Somali government. The emerging US strategy on Somalia—borne out in stated policy, expanded covert presence and funding plans—is two-pronged: On the one hand, the CIA is training, paying and at times directing Somali intelligence agents who are not firmly under the control of the Somali government, while JSOC conducts unilateral strikes without the prior knowledge of the government; on the other, the Pentagon is increasing its support for and arming of the counterterrorism operations of non-Somali African military forces.

A draft of a defense spending bill approved in late June by the Senate Armed Services Committee would authorize more than $75 million in US counterterrorism assistance aimed at fighting the Shabab and Al Qaeda in Somalia. The bill, however, did not authorize additional funding for Somalia’s military, as the country’s leaders have repeatedly asked. Instead, the aid package would dramatically increase US arming and financing of AMISOM’s forces, particularly from Uganda and Burundi, as well as the militaries of Djibouti, Kenya and Ethiopia. The Somali military, the committee asserted, is unable to “exercise control of its territory.”

That makes it all the more ironic that perhaps the greatest tactical victory won in recent years in Somalia was delivered not by AMISOM, the CIA or JSOC but by members of a Somali militia fighting as part of the government’s chaotic local military. And it was a pure accident.

Late in the evening on June 7, a man whose South African passport identified him as Daniel Robinson was in the passenger seat of a Toyota SUV driving on the outskirts of Mogadishu when his driver, a Kenyan national, missed a turn and headed straight toward a checkpoint manned by Somali forces. A firefight broke out, and the two men inside the car were killed. The Somali forces promptly looted the laptops, cellphones, documents, weapons and $40,000 in cash they found in the car, according to the senior Somali intelligence official.

Upon discovering that the men were foreigners, the Somali NSA launched an investigation and recovered the items that had been looted. “There was a lot of English and Arabic stuff, papers,” recalls the Somali intelligence official, containing “very tactical stuff” that appeared to be linked to Al Qaeda, including “two senior people communicating.” The Somali agents “realized it was an important man” and informed the CIA in Mogadishu. The men’s bodies were taken to the NSA. The Americans took DNA samples and fingerprints and flew them to Nairobi for processing.

Within hours, the United States confirmed that Robinson was in fact Fazul Abdullah Mohammed, a top leader of Al Qaeda in East Africa and its chief liaison with the Shabab. Fazul, a twenty-year veteran of Al Qaeda, had been indicted by the United States for his alleged role in the 1998 US Embassy bombings and was on the FBI’s “Most Wanted Terrorists” list. A JSOC attempt to kill him in a January 2007 airstrike resulted in the deaths of at least seventy nomads in rural Somalia, and he had been underground ever since. Secretary of State Hillary Clinton called Fazul’s death “a significant blow to Al Qaeda, its extremist allies and its operations in East Africa. It is a just end for a terrorist who brought so much death and pain to so many innocents.”

At its facilities in Mogadishu, the CIA and its Somali NSA agents continue to pore over the materials recovered from Fazul’s car, which served as a mobile headquarters. Some deleted and encrypted files were recovered and decoded by US agents. The senior Somali intelligence official said that the intelligence may prove more valuable on a tactical level than the cache found in Osama bin Laden’s house in Pakistan, especially in light of the increasing US focus on East Africa. The Americans, he said, were “unbelievably grateful”; he hopes it means they will take Somalia’s forces more seriously and provide more support.

But the United States continues to wage its campaign against the Shabab primarily by funding the AMISOM forces, which are not conducting their mission with anything resembling surgical precision. Instead, over the past several months the AMISOM forces in Mogadishu have waged a merciless campaign of indiscriminate shelling of Shabab areas, some of which are heavily populated by civilians. While AMISOM regularly puts out press releases boasting of gains against the Shabab and the retaking of territory, the reality paints a far more complicated picture.

Throughout the areas AMISOM has retaken is a honeycomb of underground tunnels once used by Shabab fighters to move from building to building. By some accounts, the tunnels stretch continuously for miles. Leftover food, blankets and ammo cartridges lay scattered near “pop-up” positions once used by Shabab snipers and guarded by sandbags—all that remain of guerrilla warfare positions. Not only have the Shabab fighters been cleared from the aboveground areas; the civilians that once resided there have been cleared too. On several occasions in late June, AMISOM forces fired artillery from their airport base at the Bakaara market, where whole neighborhoods are totally abandoned. Houses lie in ruins and animals wander aimlessly, chewing trash. In some areas, bodies have been hastily buried in trenches with dirt barely masking the remains. On the side of the road in one former Shabab neighborhood, a decapitated corpse lay just meters from a new government checkpoint.

In late June the Pentagon approved plans to send $45 million worth of military equipment to Uganda and Burundi, the two major forces in the AMISOM operation. Among the new items are four small Raven surveillance drones, night-vision and communications equipment and other surveillance gear, all of which augur a more targeted campaign. Combined with the attempt to build an indigenous counterterrorism force at the Somali NSA, a new US counterterrorism strategy is emerging.

But according to the senior Somali intelligence official, who works directly with the US agents, the CIA-led program in Mogadishu has brought few tangible gains. “So far what we have not seen is the results in terms of the capacity of the [Somali] agency,” says the official. He conceded that neither US nor Somali forces have been able to conduct a single successful targeted mission in the Shabab’s areas in the capital. In late 2010, according to the official, US-trained Somali agents conducted an operation in a Shabab area that failed terribly and resulted in several of them being killed. “There was an attempt, but it was a haphazard one,” he recalls. They have not tried another targeted operation in Shabab-controlled territory since.