In Fort Lamy, French Equitorial Africa, idealist Morel (Trevor Howard)launches a one-man campaign to preserve the African elephant from extinction, which he sees as the last remaining "roots of Heaven." At first, he finds only support from Minna (Juliette Greco), hostess of the town's only night club, who is in love with him, and a derelict ex-British Army Major, Forsythe (Errol Flynn.) His crusade gains momentum and he is soon surrounded by an odd assortment of characters: Cy Sedgewick (Orson Welles), an American TV commentator who becomes impressed and rallies world-wide support; a U.S. photographer,Abe Fields (Eddie Albert), who is sent to do a picture story on Morel and stays on to follow his ideals; Saint Denis (Paul Lukas), a government aide ordered to stop Morel; Orsini (Herbert Lom), a professional ivory hunter whose vested interests aren't the same as Morel's; and Waitari (Edric Connor), leader of a Pan-African movement who follows Morel only for the personal good it will do his own campaign.

In the town of Biondi in French Equatorial Africa, Morel launches a campaign to save the majestic elephant herds from hunters, poachers and zoo collectors. Morel's crusade is rebuffed by the territorial governor and a missionary priest, who both refuse to sign his petition on the grounds that their concern is the betterment of humankind, not animals. At the local café, Saint Denis, a government official, ridicules Morel and declares that the killing of elephants is too profitable to be outlawed. The only people who agree to sign Morel's petition are Minna, the barmaid who was forced into prostitution by the Germans during World War II, and Forsythe, an incorrigible drunk. When his civil endeavor fails, Morel institutes a terrorist campaign aimed at the hunters and people who collect elephants for zoos. Morel attracts the attention of famed U.S. television broadcaster Cy Sedgewick when he shoots him in the rear while Sedgewick is rhapsodizing about hunting elephants. Sensing a story, Sedgewick sides with Morel and begins to champion his cause. Drawn by Sedgewick's interest, busloads of journalists descend on the town. Suspecting that Morel has forged an alliance with Waitari, a native leader who advocates an end to imperialism, the governor sends Saint Denis to find Morel. In the African bush, Saint Denis meets Morel and his small band of supporters: Danish scientist Professor Peer Quist, the Baron, a German nobleman, and Waitari, who has decided to co-opt Morel's crusade to argue the cause of African nationalism. After Morel refuses to surrender until the elephant killing stops, Saint Denis comes to respect him and begins to question the motives of the government. Back in Biondi, Minna offers Saint Denis sexual favors in exchange for protecting Morel, whom she now admires. Saint Denis refuses her offer and instead sends her to Morel to convince him to surrender before he is killed. Enlisting Forsythe's help, Minna loads a jeep with supplies and drives into the bush. Along the way, Forsythe confesses that he is tormented because during the war, as a British officer, he passed on strategic information to the enemy rather than face death like the rest of his battalion. Led by a witch doctor friend of Saint Denis', Forsythe and Minna reach Morel, who confides that his obsession with elephants began when he was a prisoner in a German POW camp, because thinking about the massive beasts helped him to survive. At daybreak, Morel and his band sneak back to Biondi, where Morel enlists a native printer to publish a leaflet outlining his demands. Morel then crashes a party at the Orsini house and publicly humiliates Madame Orsini, a wealthy white hunter, by having her spanked for her crimes. Irate that the cause of African nationalism has been excluded from the manifesto, Waitari breaks ranks with Morel. The drought has driven the elephants to congregate at a lake, and Morel and his band follow them there. Soon after, Abe Fields, an American photojournalist covering the Morel story, crash lands at the lake in a plane. That night, truckloads of ivory poachers bearing machine guns come to the lake to massacre the elephants, and to save the herd, Morel causes a stampede. In retaliation, the poachers fire at Morel and his men, killing Forsythe and the Baron and capturing the others. As the poachers pile the tusks into their trucks, Waitari and his followers arrive to advocate Morel's execution. After Fields convinces them to reconsider, Waitari frees Morel and his band. When word comes that the Congo Congress has refused to outlaw elephant hunting, Morel, defeated and disillusioned, decides to turn himself in, and Fields joins them on their arduous trek through the barren countryside. During a brutal wind storm, Minna, weak and feverish, collapses and is carried the rest of the way on a stretcher. As Morel continues on his journey, he is joined by admiring supporters, and by the time he reaches Biondi, the ranks have swollen to become a multitude. When Morel emerges from the bush, the police chief, overwhelmed by Morel's show of support, allows him to pass. After saying goodbye to the ailing Minna, Morel and his burgeoning army return to the bush.