It begins with the protagonist, an upper class gentleman named Edward Prendick, finding himself shipwrecked in the ocean. A passing ship takes him aboard, and a man named Montgomery revives him. He explains to Prendick that they are bound for an unnamed island where he works, and that the animals aboard the ship are traveling with him. Prendick also meets a grotesque, bestial native named M'ling, who appears to be Montgomery's manservant.
When they arrive on the island, however, both the captain of the ship and Montgomery refuse to take Prendick with them, stranding him between the ship and the island. The crew pushes him back into the lifeboat from which they rescued him. When they see that the ship truly intends to abandon him, the islanders take pity and end up coming back for him. When they arrive at their island, Montgomery introduces Prendick to Doctor Moreau, a cold and precise man who conducts research on the island. After unloading the animals from the boat, they decide to house Prendick in an outer room of the enclosure in which they live. Prendick is exceedingly curious about what exactly Moreau researches on the island, especially after he locks the inner part of the enclosure without explaining why. Prendick suddenly remembers that he has heard of Moreau, and that he had been an eminent physiologist in London before a journalist exposed his gruesome experiments in vivisection.
The next day, Moreau begins working on a puma, and its anguished cries drive Prendick out into the jungle. As he wanders, he comes upon a group of people who seem human but have an unmistakable resemblance to hogs. As he walks back to the enclosure, he suddenly realizes he is being followed. He panics and flees, and, in a desperate attempt at defense, he manages to stun his attacker, a monstrous hybrid of animal and man. When he returns to the enclosure and questions Montgomery, Montgomery refuses to be open with him. After failing to get an explanation, Prendick finally gives in and takes a sleeping draught.
Prendick awakes the next morning with the previous night's activities fresh in his mind. Seeing that the inner door has been left unlocked, he walks in to find a humanoid form lying in bandages on the table before he is ejected by a shocked and angry Moreau. He believes that Moreau has been vivisecting humans and that he is the next test subject. He flees into the jungle, where he meets an Ape Man who takes him to a colony of similarly half-human/half-animal creatures. The leader, a large gray thing named the Sayer of the Law, has him recite a strange litany called the Law that involves prohibitions against bestial behavior and praise for Moreau. Suddenly, Moreau bursts into the colony, and Prendick escapes out the back into the jungle. He makes for the ocean, where he plans to drown himself rather than allow Moreau to experiment on him. Moreau and Montgomery confront him, however, and Moreau explains that the creatures, the Beast Folk, are animals he has vivisected to resemble humans. Prendick goes back to the enclosure, where Moreau explains to him that he has been on the island for eleven years now, striving to make a complete transformation from animal to human. Apparently, his only reason for the pain he inflicts is scientific curiosity. Prendick accepts the explanation as it is and begins life on the island.
One day, as he and Montgomery are walking around the island, they come across a half-eaten rabbit. Eating flesh and tasting blood is one of the strongest prohibitions in the Law, so Montgomery and Moreau become very worried. Moreau calls an assembly of the Beast Men. He identifies the Leopard Man (the same one that chased Prendick the first time he wandered into the jungle) as the transgressor. The Leopard Man flees, but when the group corners him in some undergrowth, Prendick takes pity and shoots him, sparing him a return to the operating table in Moreau's "House of Pain". Prendick also believes that, although the Leopard Man was seen breaking several laws such as drinking water bent down like an animal, chasing men (i.e. Prendick) and running on all fours, the Leopard Man was not solely responsible for the deaths of the rabbits, but it was also the Hyena-Swine, the other most dangerous beast man on the island. He doesn't, however, tell anyone this. Moreau is furious that Prendick killed the Leopard Man but can do nothing about the situation.
As time passes, Prendick begins to deaden himself to the grotesqueness of the Beast Folk. One day, however, he is shaken out of this stagnation when the puma rips free of its restraints and escapes from the lab. Moreau pursues it, but the two end up killing each other. Montgomery falls apart, and having gotten himself quite drunk, decides to share his alcohol with the Beast Men. Prendick tries to stop him, but Montgomery threatens violence and leaves the enclosure alone with bottle in hand.
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