U.S. AFRICOM (Africa Command) reported that it had carried out 679 activities (missions, programs, and exercises) in 2014. This includes training, advising, intelligence gathering (via UAV, manned aircraft or people on the ground), logistical or technical assistance and so on. That was 23 percent more than in 2013 and four times as many as 2008 the first year AFRICOM was in charge of all American military activities in Africa. The number of activities (many of them classified SOCOM missions) is expected to be more than 20 percent higher in 2015. AFRICOM is in greater demand throughout Africa because of the growing threat of Islamic terrorism and the greater participation of African troops in peacekeeping operations (mainly within Africa.) American troops have long trained foreign troops in peacekeeping techniques and has a reputation for doing it well. Another increasingly popular AFRICOM activity is aerial surveillance, using manned aircraft, UAVs and satellites. AFRICOM also provides help with logistics and planning military and security operations. The armed forces in most African nations needs help in these areas and finds that the American aid works and is usually free. Such a deal.
AFRICOM headquarters is in Germany, where 1,500 personnel command and coordinate a much larger force of American troops and civilians operating in dozens of African countries. AFRICOM has been unable to establish its headquarters anywhere in Africa and has been in a temporary headquarters in Germany until someplace in Africa was found. Failing that, the plan was to move the headquarters back to the U.S. But AFRICOM commanders pointed out that Germany was closer to African hotspots than the United States and, more importantly, closer to European nations that are also involved in African peacekeeping and counter-terror operations. Germany is also in the same time zone as most of Africa.
AFRICOM is similar in organization to other commands (CENTCOM, for the Middle East, and SOUTHCOM, for Latin America and so on). AFRICOM coordinates all American military operations in Africa. Before AFRICOM was created those operations were coordinated between two other commands (the one covering Europe and the one covering Latin America). The establishment of AFRICOM means more money for counter-terror operations in Africa and more long range projects. No country in Africa had sufficient infrastructure for AFRICOM headquarters and few wanted to risk the political blowback from hosting a major American military headquarters. This is not uncommon, as few of these headquarters are located outside the United States.
This is an organization that is spread around a vast continent. Office and support facilities for the AFRICOM has always had its headquarters outside Stuttgart, Germany. Finding a home in an African country is probably never going to happen. Instead there are a growing number of official and unofficial AFRICOM bases throughout the continent.
There is one official U.S. military base in Africa, in Djibouti. France and the United States SOCOM (Special Operations Command) have had special operations forces (commandos and special aircraft) stationed in Djibouti, which is next to northern Somalia, for years. France has had commandos there for over a decade and the U.S. moved in after September 11, 2001. But you don't hear much about this corner of the War on Terror, despite the numerous terror groups in the region (especially Yemen and Somalia). Why is that? Well, it's complicated.
France has been building up their special operations capability in Djibouti since 2006 in anticipation of problems in Eritrea and Somalia, both of which are involved in disputes with Ethiopia. The Addis Ababa (Ethiopia)-Djibouti railroad is pretty lucrative for Djibouti and France (because it is Ethiopia's main outlet to the sea), and fighting between Ethiopia and either of its neighbors could create problems there. American Special Forces in Djibouti have a base near the main French one. It's pretty easy to spot on Google Earth. Less easy to spot is the fact that France and SOCOM also have access to one or more Ethiopian air bases. American UAVs operate from Ethiopia and Djibouti. The UAVs are sometimes armed with missiles. Some of these armed UAVs are believed to have (until early 2015) also operated out of Yemen air bases. When not attacking al Qaeda targets in Yemen, these UAVs are sometimes seen across the water in Somalia. UAVs are now operating out of a new base in Niger, to cover Mali.
U.S. forces in Djibouti were increased after resistance collapsed in Iraq during 2008. By 2010 there was even a small, and unofficial, CIA base in Mogadishu, the traditional capital of Somalia. The CIA, and similar outfits from other nations, also work from Djibouti. But most of the effort is directed at monitoring what is going on in the region (mainly Somalia and Yemen but also Eritrea, Nigeria, Kenya, Mali and Ethiopia), not at interfering with the local terrorists. Not much, anyway. The Djibouti base also supports operations throughout the Sahel (the semi-desert strip between the North African desert and the Central African jungles, which stretches from the Atlantic to Somalia).
The U.S. also has a number of other airports in central and southern Africa where it has agreements to quietly allow its military and contractor aircraft to operate. American warplanes (especially the very-long range F-15E) operate out of Persian Gulf air bases and have apparently carried out smart bomb attacks in Yemen, Somalia, and perhaps elsewhere in Africa. Throughout the region there are often large explosions at night. If a smart bomb was dropped from a high enough altitude, there would just be the explosion and yet another mystery no one was keen to solve.