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
Gulliver starts out this novel as a fairly average guy, educated in a useful profession. When he becomes shipwrecked on Lilliput, he sees a number of political intrigues that mimic those of his home country, but he doesn't seem to recognize the similarities because the Lilliputians are so small – insignificant, even. Then, he heads to Brobdingnag, where he starts getting a little insecure. But it's only upon Gulliver's arrival at Houyhnhnm Land that he really confronts how much he has grown to despise people.
Act II
The second act is the part of the story where everything seems as far as possible from an ending. If we consider the conclusion of Gulliver's Travels to be Gulliver's unhappy hatred of mankind, then he is probably furthest away from that conclusion when he happily hates people. Gulliver's time in Houyhnhnm Land seems like an ideal solution to his misanthropy, but it cannot last, because the Houyhnhnms don't want such an unpleasant, dangerous creature around them. So Gulliver is expelled from horse-faced paradise.
Act III
Act Three is supposed to be the moment in a book when all of the plot's problems get solved. For Gulliver, there is no solution: he is a man and he cannot escape that. He thought he could for a time, living among the horses, but at the end of his travels, his only answer is to seclude himself from both his family and the world – and to talk to his horses for four hours each day.