In my honest opinion, these would be the most plausable (but still highly, highly unlikely) situations in which an African country conquers another:
1. Shortly after Independence in 1961, Sir Milton Margai is ousted in a coup in Sierra Leone. Liberia comes to the aid of Sierra Leone and invades. They create a puppet regime (True Whig Party of Sierra Leone). Once it becomes clear that the TWP of Liberia and the TWP of Sierra Leone are facing the same opposition (ethnic natives who loathe the ruling class who are decendents of former slaves) they merge their country into "The United States of Liberia".
2. When Gambia balks at moving closer to a Senegambian Union in 1989 the Senagalese military invades and takes over Gambia.
3. In 1966 after the Tutsi led coup ousts the monarch of Burundi, Hutu led Rwanda invades and eventually conquers Burundi. They annex it and create a unified Hutu Republic.
4. After the Ugandan-Tanzanian war Tanzania absorbs Uganda.
5. South Africa annexes South West Africa at some point.
6. Morroco doesn't stop at the Mauritanian border after the Green March and conquers Mauritania as well.
7. After Kaliba ousts Mobutu he calls for a Greater Congo. His invasion is repealed but Kinsasha falls to the Rep. of Congo, who decide they like the "greater Congo" idea.
8. Ghana invades Togo
9. The 1958 Djibouti referendum on union with Solmalia goes in favor of a union with Somalia. Coup follows and military dictatorship declares independence, calling the referendum void. Somalia (which has not yet slipped into anarchy) invades and conquers Djibouti, with France's blessing.
Some of these are more plausable than others (although I would say all but #9 and maybe #3 are pretty unlikely), but these are my scenarios where we could see an African country invade another and conquer it.