After being out to sea for six months without seeing land, the whaling ship The Dolly stops in the Marquesas Islands located in the South Pacific. Tired of a life of drudgery and abuse on board, the narrator, later called Tommo, decides to flee the ship with a fellow shipmate, Toby. The two men plan to hide on the island of Nukuheva, eating tropical fruits until they can catch a ride on a better boat. They must be careful while hiding, though, since the island is partially populated by the Typees, a violent tribe known for being cannibals.
The two men make their escape while the crew is on shore leave. After spending several cold and wet nights on the island mountain, Tommo and Toby spot a beautiful valley below. They are hungry, cold, and Tommo also feels feverish due to an injury to his leg. They decide to descend into the valley even though they are not sure if it is the home of the friendly Happar tribe or that of the dreaded Typee. After a dangerous descent, which involves scaling a steep ravine and jumping onto a tree from a cliff above, the two men are in the heart of the valley. They spot a tree of tropical fruit and then a young native man and woman. Because of their desperation, they approach the natives and offer them a piece of calico cloth. Initially, Toby and Tommo happily think that the natives are Happars, not Typees. After arriving in their nearby village however, a stern chief, Mehevi, asks Tommo, "Typee" or "Happar"? Knowing that he must choose correctly, Tommo suddenly changes his mind and says "Typee." His guess is right and the surrounding natives start chattering happily. The Typees offer Tommo and Toby food and a place to sleep. Mehevi orders a man named Kory-Kory to be Tommo's servant. Tommo immediately feels deeply attracted to a beautiful maiden named Fayaway.
In their initial days with the Typees, Tommo quickly learns to enjoy the pleasures of their lifestyle. Kory-Kory feeds Tommo by hand, carries him everywhere due to his injured leg, and bathes him each morning in the nearby stream. Despite the Typees's hospitality though, neither Toby nor Tommo is entirely free from their fear about cannibalism. When they are served meat for the first time, Toby instantly declares that it is roast human baby and refuses to eat it. Tommo later discovers that it is actually roast pork, but he still remains apprehensive that the Typees plan to do him harm. Tommo's leg injury also continues to be painful and crippling. Eventually, Toby starts for Nukuheva to get Tommo some European medicine, but has to turn back after an altercation with nearby Happars. Soon after, some foreign ships appear in the Typee Bay and Toby goes with the Typees to greet them. He never returns and Tommo is given only inconclusive answers about where he went. Tommo occasionally worries that the Typees killed and ate Toby, since he has no other explanation.
With time though, Tommo begins to relax and truly enjoy Typee life. As he does so, his leg heals. He spends his days walking with Fayaway or Kory-Kory. He bathes in the morning with a group of half-dressed maidens, sleeps much of the day, and chats with Mehevi at the Ti, a religious location reserved only for men. Tommo describes the Typee culture in depth, including their religious, marital, and social practices. He believes that the Typees are more civilized than Europeans and Americans, even though the latter call natives "savages." Actually, Tommo finds that natives live with more honesty, truth, and goodness than Europeans. Their one major flaw is that they sometimes act as cannibals, but many European cultures have engaged in comparably brutal acts, Tommo notes.
Despite Tommo's happiness, he still worries about the Typees's intentions towards him. When the Typees express a desire to tattoo him, Tommo becomes terribly distressed at the thought and it is only through extensive begging that the tattooing is not enforced. The pressure to be tattooed hastens Tommo's desire to escape. This desire is reinforced when Tommo sees the natives holding three shrunken human heads, one of which belongs to a white man. Soon after, Tommo positively learns that the Typees are cannibals. After a battle with the Happars, a feast is held from which Tommo is carefully excluded. Later, though, he sees part of a half-eaten body and knows that the Typees ate the dead Happars. He then thinks about escape constantly.
Tommo's escape comes when a Nukuheva native, Karakoee, comes to the Typee Bay trying to buy Tommo's freedom for an Australian whaling captain. When the natives are not paying close attention, Tommo leaps towards Karakoee and they start rowing away. Several native men swim after them in an effort to overturn their boat, but Tommo disables one of the ferocious chiefs, Mow-Mow, with a forceful blow. Tommo and Karakoee make their escape. When he knows he is free, Tommo faints. Later, however, he entertains his new crew on the Australian ship with tales of his adventures.
In the sequel "the story of Toby," Toby's mysterious disappearance is explained. He disappeared when a European resident of Nukuheva, Jimmy, arrived and negotiated for his freedom. Toby believed that Jimmy truly wanted to help him, but Jimmy actually was simply working for a whaling ship in need of a crew. After they reached Nukuheva, Toby learned that no one would go back for Tommo as they had promised. He was forced to leave on the ship. Until the publication of Typee, he had believed that his friend, the narrator, was dead.