For a three-act plot analysis, put on your screenwriter’s hat. Moviemakers know the formula well: at the end of Act One, the main character is drawn in completely to a conflict. During Act Two, she is farthest away from her goals. At the end of Act Three, the story is resolved.
Act I
Act I lasts from the beginning of the book to the point when Prendick discovers the vivisection of the puma (whom he takes to be human) and flees from the company of Moreau and Montgomery. The stage is set—a lonely island in the midst of the Pacific—the players are introduced—both the main actors and the beastly secondary players—and the conflict is in full-swing. There's no going back when Prendick discovers that he's shipwrecked himself right onto the scene of a horror-movie.
Act II
Act II begins when the protagonist is introduced to the Beast People and things go from bad to worse. Although Prendick finds out what is happening on the island, the situation unravels as the Masters lose control of the Beasts and the relationships between everyone are strained and polarized (which is a fancy word for something becoming more extreme). The act ends with the death of Moreau and Prendick's realization that given Montgomery's drinking problem, he's now the sharpest knife left in the drawer and that it's up to him to salvage the whole mess.
Act III
Act III is the act that resolves everything. Prendick is left by himself on the island, thanks to his pals Montgomery and M'ling going off and dying and his loyal companion Dog-Man kicking the bucket as well. Our protagonist is alone amongst hostile creatures that are getting wilder and more dangerous by the day and without Bear Grylls' mad skills at that. Lucky for him, a dinghy washes ashore with two corpses inside (not so lucky for those guys). Not feeling particularly picky, Prendick takes the boat and manages to get picked up by a ship. He returns to England, alive but emotionally scarred by his experiences.