The United States has intelligence operations, often run through the military, throughout the African continent, according to the Washington Post, which "pieced together descriptions of the surveillance network by examining references to it in unclassified military reports, U.S. government contracting documents and diplomatic cables released by WikiLeaks, the anti-secrecy group. Further details were provided by interviews with American and African officials, as well as military contractors."
The operations are run largely out of African military bases and small civilian airports, with refueling often occurring "on isolated airstrips favored by African bush pilots, extending their effective flight range by thousands of miles." While some Predator and Reaper drones are used (likely largely in Somalia), most of the surveillance planes are manned and disguised as civilian aircraft, and the Post reports a central hub of the operations in Ougadougou, the capital of Burkina Faso. America established its presence there in 2007 for "medical evacuation and logistics requirements." Other bases are in Mauritania, Djibouti (where more than 200 Marines are based for forward operations in the Middle East), Uganda (where a hundred U.S. troops are hunting the war criminal Joseph Kony), Ethiopia, Kenya and the Seychelles. The U.S. hopes to expand its facilities there and open new ones elsewhere.
The military admits to air strikes and raids in Somalia (where the Islamist terror group al-Shabab briefly held power in Mogadishu), but otherwise they say "they generally limit their involvement to sharing intelligence with allied African forces so they can attack terrorist camps on their own territory." A self-declared independent Islamist state in the north of Mali that arose in the wake of Western intervention in Libya, is one area of interest, the growing threat of the Islamist terror group Boko Haram in Nigeria another. The U.S. is interested in setting up a military presence in South Sudan, too, to help hunt down Joseph Kony but also to bring itself closer to the growing conflict between Sudan and the recently independent South Sudan.
The Washington Post reports that "operations have intensified in recent months, part of a growing shadow war against al-Qaeda affiliates and other militant groups [on the continent]", and Army General Carter Ham, head of the U.S. Africa Command (headquartered in Germany) told Congress the military wants to expand its intelligence, surveillance and reconnaissance operations further on the continent. But, the Washington Post warns:
The creeping U .S. military involvement in long-simmering African conflicts, however, carries risks. Some State Department officials have expressed reservations about the militarization of U.S. foreign policy on the continent. They have argued that most terrorist cells in Africa are pursuing local aims, not global ones, and do not present a direct threat to the United States.
Guerrilla groups on the African continent, generally, have neither the means nor the desire to target the United States, though enough intervention may change the desire and maybe even eventually the means (still a lot of missing weapons post-Libya)
The Post also relays the story of one private contractor working for the U.S. in Africa being picked up by air marshals on a Paris-to-Atlanta flight after saying he had dynamite in his boots and laptop and "mumbling incoherently" about secret operations in Africa. He was found not guilty by reason of temporary insanity for the disruption.