An English spinster, Rose (Katharine Hepburn
), is the sister of a missionary, Rev. Samuel Sayer (Robert Morley
). The two Christian missionaries are in a remote African village with grass huts and a little wooden church, which is located somewhere deep in a German African colony during WWI near the Ulanga River. The German war machine appears to brutally start burning the little straw hut village, killing the native women and children while kidnapping the African men, and just as quickly the German terror vanishes. When the smoke clears from the burning village, all is in ruin. The meek and fragile Rev. Samuel Sayer is so distraught by what he has just witnessed he kills himself. Rose is left all alone to fend for herself;she is lost in despair. There is no safety here, and the German threat is all around. There is no way out except to travel south down the dangerous and unforgiving Ulanga River. The river leads to Lake Victoria and possible freedom. Except for the last danger, which is the Louisa - a German gunship that patrols the Tanganyika shore of the lake up to the southern mouth of the river. The Ulanga is filled with dangers like animals that can eat you, rocks and white water rapids that can smash and sink a boat. It has only been successfully navigated once by a map maker named Spangler a hundred years ago and no one since has repeated the feat.
Rose is straggling about the burnt village in shock and despair from her brother's suicide when a Mr. Charlie Allnut (Humphrey Bogart
) shows up out of nowhere to save her. This scruffy old gin-swigging rummy is a boat captain who is unshaven and crusty. Mr. Allnut is there to deliver mail and supplies to the village. Mr. Allnut travels up and down the northern part of the Ulanga on a rusty old 12-foot boat called the African Queen. The boat barely runs, powered by a small antique steam engine on its last legs kept together and encouraged to run with a few well placed kicks and bangs from a hammer by Mr. Allnut. Mr. Allnut buries Rev. Sayer and takes Rose to the African Queen for safety before the Germans come back. While on the African Queen Rose attempts to convince Mr. Allnut they should go south down the Ulanga and sink the Louisa. Mr. Allnut thinks the spinster is a crazy old maid and tells her so. And Rose thinks Mr. Allnut is washed-up rummy good for nothing coward unfit to be a captain. As impossible as it may seem Mr. Allnut decides to follow her suggestion because its the only way to avoid the Germans, and probably the only way to shut Rose up and stop her from nagging on and on about her crazy plan to fight the German navy.
During the first few days aboard the African Queen navigating the Ulanga they annoy each other to the point of being disgusted. Rose reads her bible while Mr. Allnut drinks rum from a generous supply he has on board until he passes out every day. Rose decides to dump all of Mr. Allnuts bottles of gin into the river one morning while Mr. Allnut is still passed out. When Mr. Allnut awakes, he is emotionally destroyed by the thought of no more booze. How could you, Miss? Mr. Allnut asks over and over as the African Queen smokes and tugs along the Ulanga. Rose decides to stop talking to Mr. Allnut and gives him the silent treatment until he gives in to her plan to sink the Louisa. Mr. Allnut continues to talk to Rose even though Rose refuses to acknowledge his existence on the little boat. Mr. Allnut pretends he doesn't care even though the silence is slowing killing him. It is apparent they cannot stand each others company. Finally Mr. Allnut can't take the silence anymore and agrees to Rose's impossible plan to sink the Louisa using home made torpedoes made by Mr. Allnut. Mr Allnut says he can make them from the supplies on the boat - explosives and two gas canisters used for welding.
As the two strangers sail down Ulanga River like great map makers before them and determined to sink the Louisa, Rose is impressed by Mr. Allnut's abilities and admires his seamanship when they hit big white water and how he skillfully navigates past the dangerous rocks. They ride into some really rough white water that causes Rose to feel aroused by the thrill of the ride. Not understanding the experience she compares it to a thrilling sermon delivered by her brother when the holy ghost consumed him. The spiritual excitement overcomes her as she describes her excitement to Mr. Allnut. Rose and Mr. Allnut survive a second and more dangerous set of white water rapids, along with extra dangers from African guerrillas shooting at them from the banks of the river hoping to kill them and capture the African Queen. When they realize they have survived certain death again they start hugging and kissing. After they kiss, they realize they are in love. It's implied they are lovers that afternoon after much flirting and a quick nap. However, their troubles are not over as the African Queen breaks down and they work as a team to fix it. Mr. Allnut shaves, baths and listens to Rose read the good book. They make tea and find they adore each others company. They call each other dear and tell each other sweet nothings.
Nevertheless there is still more danger ahead. The river disappears, the water is shallow, and Mr. Allnut is forced to get into the mucky river and pull the African Queen by hand to higher water. Blood sucking leeches, mosquitoes, and dangerous animals torment the couple's efforts. The African Queen comes to a complete stop, stuck dead in mucky swamp water and high weeds covering any sight of land or water ways. They are lost in the weeds and can't see anything. They are disheartened and beaten and accept their doomed fate as they hold each other in exhaustion waiting to die. Passed out on the African Queen they lie there defeated. When it begins to rain and the river rises, the African Queen becomes unstuck and floats down the river only a few hundred feet from high water and the mouth of the Ulanga River. The Ulanga River is pouring into Lake Victoria and they see the Louisa gunship for the first time as it makes a routine patrol..
The two lovers are now alive again! With new hope and determination they are convinced they can now sink the Louisa. They wait in the banks of the Ulanga out of sight of the Louisa until it comes back on its routine patrol. They have fixed and fastened two homemade torpedoes to the insides of the African Queen. By cutting circle holes above the water line they can stick the tips of the torpedoes through the holes which act as battering rams that will compress on collision and ignite the explosives to explode the gas canisters when they crash into the Louisa at full speed ahead. Rose and Mr. Allnut lovingly argue about who will stay ashore while the other steers the boat into the Louisa. The hero will jump just before the collision and explosion that will sink the Louisa on impact. They both decide they would not want to live without the other so they will do it together. Rose and Mr. Allnut wait until the Louisa comes back on its patrol routine that evening and begin to plan to ram the Louisa. Building steam as the weather starts to change and the waves grow higher. The Louisa is not expecting the African Queen to even be there let alone capable of exploding and sinking the Louisa. As they steam towards the Louisa the lake begins to become rough, a rain storm squalls, and the seas begin filling the boat with water. A rogue wave turns the African Queen upside over tossing Rose and Mr. Allnut into the lake. The two are separated by another huge wave and disappear. Have they drowned? Alas, the Louisa is not sunk and the African Queen appears to be gone with the two star-crossed lovers.
The sun appears after the storm and we see Mr. Allnut is alive. He was rescued and captured by the Germans. Mr. Allnut is now standing on the Louisa's deck in the captain's office. He is being interrogated by the Louisa's captain (Peter Bull
). The captain is determined to have Mr. Allnut answer his questions. The German captain always ends each question with the threat of death and hanging to Mr. Allnut, who is depressed and despondent. Mr. Allnut answers each question and threat of death with a hopeless sigh of, who cares! Because Mr. Allnut believes his Rose has drowned. Mr. Allnut is relieved by the thought of hanging rather than live without his Rose. Suddenly he hears Rose's voice coming from a life boat that has rescued her. Mr. Allnut, thrilled that Rose is alive, decides to deny he knows her in hopes of saving her from his fated hanging by the Germans. But the very English Rose not only argues with the captain but brags how she and Charlie and the African Queen sailed down the Ulanga, and how Charlie made homemade torpedoes, and how they came within feet of sinking the Louisa by themselves and would have, but the storm saved the Louisa from their doom when the weather caused the African Queen to sink and a wave tossed them into the water. The Louisa's captain thinking them both crazy decides to hang them both. On the deck of the Louisa, Rose and Charlie stand holding hands deeply in love, happy about dying together. Standing there with the hangman's rope around their necks Charlie asks the Louisa's captain to marry them as his last request before hanging. Charlie says he really doesn't care about getting married but it would mean a lot to the Mrs. A teary-eyed Rose is thrilled by the suggestion. The Louisa's captain thinks they are both mad but reluctantly agrees to marry them. The two are so happy to be married that they don't care they are going to be hung. Just as he pronounces them man and wife the Louisa explodes. The sunken African Queen has been hit by the Louisa. Rose and Charlie find themselves swimming and the Louisa is gone. They did it. A wood plank with the name African Queen floats by and the two grab it as they swim to apparent safety. Swimming away, the two sing merrily, "There was an old fisherman..."