AFRICOM is similar in organization to other commands (CENTCOM, for the Middle East, and SOUTHCOM, for Latin America, etc). 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.
Last year the U.S. admitted what everyone already knew, American warplanes (UAVs, fighter-bombers and helicopters) have been making precision attacks on Islamic terrorists in places like Yemen and Somalia. About the same time separate revelations detailed the growing number of intelligence operations in Africa. All this can be better managed from a European headquarters.
This is an organization that is spread around a vast continent. Office and support facilities for the AFRICOM, which was created five years ago, has always had its headquarters outside Stuttgart, Germany, where it was to remain until a home could be found in an African country. That is not 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 during the last six years 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 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 apparently going to (or already is) operating out of a new base in Niger, to cover Mali.
U.S. forces in Djibouti were increased after resistance collapsed in Iraq five years ago. Now there is 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, Kenya, 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.