These operations allegedly include the rendition of suspected jihadists seized in East Africa and spirited to an underground CIA interrogation center in Mogadishu and using mercenaries to train Somali assassination teams to hit al-Shabaab, the main insurgent group and which is linked to al-Qaida.
Jeremy Scahill, who specializes in security affairs, recently spent time in Somalia and reported in The Nation that the CIA operates from a heavily guarded compound at the capital's beachside airport secured by guard towers and has its own fleet of aircraft.
The agency, he adds, has a "secret prison" under the headquarters of Somalia's National Security Agency, an arm of the dysfunctional Western-backed Transitional Federal Government which is kept in power largely by a 9,000-strong African Union peacekeeping force known as AMSOM.
Suspected al-Shabaab operatives are held there along with prisoners seized in Kenya, Uganda and other East African countries, where al-Qaida is known to operate, and secretly flown to Mogadishu.
This is all part of an expanding U.S. counter-terrorism campaign that also embraces Yemen, Pakistan and Afghanistan, even the Philippines and Indonesia.
It is spearheaded by the CIA, which has become increasingly militarized in recent years, and the U.S. military's Joint Special Operations Command.
The Americans, aided by their allies, have killed or captured dozens of senior al-Qaida chieftains over the last couple of years as this new strategy has shifted into high gear under U.S. President Barack Obama's administration.
The administration shies away from putting large conventional forces on the ground as it quits Iraq and starts drawing down forces in Afghanistan as popular support for distant wars wanes in the United States a decade and trillions of dollars after 9/11.
Instead it has stepped up the use of armed drones to kill jihadist leaders.
On the ground, Scahill says the Americans are increasingly replaying the tactics and often unsavory alliances they made with warlords and tribal chiefs in Iraq.
"Over the past year, the Somali government and AMISOM have turned to some unsavory characters in a dual effort to build something resembling a national army and, as the United States attempted to do with its Awakening Councils in the Sunni areas of Iraq in 2006, to purchase strategic loyalty from former allies of the current enemy -- in this case, al-Shabaab," Scahill reported.
"Some warlords … have been given government ministries or military rank in return for allocating their forces to the fight against al-Shabaab.
"Several are former allies of al Qaida or al-Shabaab, and many fought against the U.S.-sponsored Ethiopian invasion in 2006 or against the U.S.-led mission in Somalia in the early 1990s that culminated in the infamous 'Black Hawk Down' incident."
Among these warlords is Yusuf Mohamed Siad, a notorious paramilitary chieftain known by his nom de guerre of Indha Adde, or White Eyes. He's also known as "the Butcher."
Siad, who was allied with Islamist militants before the CIA bought him off, is now a three-star general funded by the agency and armed by the U.S.-sponsored AMISOM.
At times, Scahill reports, there are up to 30 CIA agents operating in Mogadishu. They appear to function outside the ambit of the TFG and its president, Sheik Sharif Sheik Ahmed.
The Americans reportedly have little faith in his corrupt administration in lawless Somalia, which has been without a functioning government since 1991.
The Americans appear to be focusing on building up an indigenous counter-terrorism force that they control, independently of the TFG in this 5-year-old proxy war.
That's where the mercenaries come in. They include Richard Rouget, aka Col. Sanders, a former French army officer who has fought in several African wars. He works for Bancroft Global Development, a private security company that has a 40-man team of "mentors" in Mogadishu.
Rouget and a group of former French, Scandinavian and South African military personnel help train AMISOM's Kenyan and Ugandan troops.
This has paid off, sort of. TFG forces, led by AMISOM, recently succeeded in pushing al-Shabaab out of Mogadishu in an offensive launched in May.
But that may have had more to do with crippling clan rivalries within the group than anything else.