The film takes place in German East Africa missionary in 1914. Rose and her brother Samuel are missionaries. Charlie Allnut is a riverboat captain on board the African Queen. He delivers mail and other supplies to the camp. Charlie comes with news that war has broken out in Europe between the English and the Germans. After Charlie leaves the Germans invade the camp. Samuel tries to stop them and gets hit with the butt of a rifle by a German soldier. The German’s eventually leave but Samuel seems to be unhinged, falling into a fever. He eventually dies.
Charlie returns to find Rose alone. She tells Charlie of her brother. He helps her bury him. Rose then boards the African Queen and the two discuss plans for getting to safety. Charlie is content with hiding in the jungle however Rose seems more bent on getting out. Charlie mentions a large lake downstream but the Germans are occupying it with a 100-ton steamer gunboat called the Louisa, making it impossible for the British to get through.
Rose devises a plan to sink the warship by making torpedoes with the explosives on board the African Queen and ramming the Louisa with the African Queen. Charlie views this plan as ludicrous. He explains to Rose it would be impossible to get by the German fort at Shona let alone the rapids. The river itself was only sailed once by a mapmaker named Spengler. As for making torpedoes Charlie tells Rose she doesn’t understand the complexity involved in making such a device. She ultimately convinces Charlie to head downstream.