After a prosperous three-week voyage, the schooner arrives at Mango, Tararo’s island. They prepare for the dangers they face from the island’s inhabitants. Ralph confirms that the dominant chief, Tararo, is hostile to Christianity and persecutes a small Christian community on the southern side of the island. They sail to the south side, where a canoe brings a native Christian missionary teacher aboard, dressed in European clothes and speaking excellent English. Jack takes him to the cabin for a private discussion and later reports that Avatea is alive but confined, wishes to join the Christians, is in love with a Christian chief from another island, and that Tararo will be occupied with a battle in two days.

They anchor near the Christian village that contrasts sharply with the other settlements Ralph previously encountered. The teacher and his wife host them for a meal, though the house is overrun with rats. Over the following day, the teacher gives them a tour, explains the three types of Pacific islands and the scientific theory of coral reef formation, and then describes the mission’s history on Mango, including his own arrival by swimming ashore, local customs including strangling a chief’s wives and burying the old chief alive, and how the new chief converted a week after his father’s burial, bringing his entire tribe to Christianity. Jack announces his intention to witness the upcoming battle to understand native customs firsthand, and Peterkin and Ralph agree to join him.

Ralph, Jack, and Peterkin walk two hours to a hilltop where they witness a fierce battle between two tribes. The warriors meet in open combat arranged in four ranks. The battle ends quickly when one side is routed, leaving 18 dead. The victors kill the wounded and remove portions of their brains as temple offerings. The boys return to the Christian village deeply disturbed.

The next day, accompanied by the teacher as an interpreter, they sail to Tararo’s village with several Christian villagers and display the brass gun prominently. They fire a salute and raise the British flag. A messenger eventually invites them ashore, but Tararo remains occupied with religious ceremonies. The teacher chastises Jack, Ralph, and Peterkin upon questioning the rigor of their religious beliefs. Jack, Ralph, and Peterkin decide to visit the temple.

They encounter a procession carrying the dead warriors, seated upright on planks, with a living bound prisoner among them. At the temple, surrounded by human bones and skulls, they watch in horror as a priest dissects the bodies before they are placed in an earth oven. The procession then moves to a nearby construction site where the living prisoner is buried alive in a hole beside a house post as a foundation ceremony. Sickened, Jack hurries them away.

The boys rejoin the teacher just as Tararo arrives on the beach. Through the teacher, Jack requests Avatea’s release, citing his previous assistance to Tararo’s people. Tararo refuses, explaining he has already promised her to another powerful chief whose deputy is currently on the island. As Indigenous people pile vegetables on the beach as a ceremonial gift, Avatea is brought forward and placed atop the heap. The teacher whispers that she is about to be sacrificed. Jack immediately rushes forward, drags Avatea from the pile, seizes a war club, and challenges the entire assembled tribe to combat.

The teacher intervenes, appealing to Tararo’s sole authority to decide Jack’s fate. Tararo halts his warriors, declares that Avatea will not be sent away for three days, but demands Jack surrender. Jack accepts and surrenders. Tararo announces Jack will remain personally free but the schooner is detained.

Aboard the schooner, the teacher reveals an escape plan: they must abandon the vessel and paddle Avatea fifty miles south to a Christian island where her lover, a chief, lives. The teacher will remain behind to divert suspicion, fully aware he may be killed. He warns of extreme danger, but Jack accepts, expressing faith in divine protection. That night they meet Avatea and learn she has learned some English. She agrees to attempt the escape, and they arrange to depart the following night.

The following night, the boys row silently to the rendezvous with Avatea, load provisions into a prepared canoe, bid farewell to the teacher, and paddle into the open sea heading south. They paddle continuously through the night and the following day. When Peterkin spots a large war-canoe in pursuit they paddle toward what appears to be land but proves to be a fog bank. The war-canoe overtakes them, rams their vessel, and hurls them all into the sea. Ralph awakens bound in the bottom of the war-canoe with Jack and Peterkin. They are given neither food nor water during the return voyage.

Upon reaching Mango, they are dragged before Tararo. Jack defiantly states his only regret is failing to save Avatea and that he would attempt it again. Tararo cancels his debt to Jack and sentences all three to death. They are imprisoned in a cave with their wrists bound. Later, as guards lead them in a procession toward the temple of sacrifice, a violent hurricane strikes. Everyone scatters, and the teacher cuts their bonds, urging them to seek shelter.

They spend the night and the following day in a cave while the hurricane rages. When it subsides, they search the devastated village for food, then attempt to flee into the mountains, but three warriors recapture them. Jack fights back but is quickly overpowered, and they are again bound and thrust into their prison cave.

For a month, the boys remain imprisoned in the dark cave, visited only by a guard who brings rations. Their emotional state deteriorates through distinct phases: terror at each approaching footstep, then agitation, and finally despair in which they wish for death. They find occasional solace in reminiscing about the past but rarely discuss the future. Ralph notes the greatest change in Peterkin, who stops joking.

One morning, their jailer unexpectedly enters with a knife and cuts the bonds from their wrists, then gestures for them to leave. They walk out and find the teacher waiting for them. He explains that another missionary has arrived on Mango, and Tararo has converted to Christianity. Tararo is about to hold a ceremony to burn their wooden idols. Dazed by the brilliant sunlight after their long confinement, the boys shout with overwhelming joy as nearby Indigenous people respond enthusiastically and form a procession to escort them to Tararo’s dwelling.

Before Tararo’s house, thousands of assembled islanders surround a pile of wooden idols ready to be burned. An English missionary greets the boys warmly and thanks God for guiding him to the island in time. Tararo confirms they are free to depart and offers provisions. When Jack inquires about Avatea, the missionary points to a group where she stands beside a chief who arrived that morning to negotiate for her release. They are to be married in a few days. Avatea’s betrothed makes a formal speech thanking Jack for risking his life for her, and Jack responds with a brief, awkward reply before retreating into the crowd.

Jack announces they should sail home to England as soon as possible. Peterkin insists on first witnessing the destruction of the idols, and moments later the pile is set alight amid the cheers of the islanders.

Ralph muses on what it means for things to come to an end. They then resolve to accept three volunteers to help sail the vessel to Tahiti, where they hope to recruit a full crew for the voyage home. Before departing, the missionary explains that a storm had driven him to Mango, where Tararo soon sought conversion and persuaded his people to follow. In the boys’ remaining days on the island, the Indigenous people begin constructing a church and new cottages. After Avatea’s wedding, she and her husband depart, accompanied by the teacher.

The boys find everything as it was in the schooner and raise the sails. The missionary and thousands of islanders gather on shore to bid them farewell, and as the vessel glides through the lagoon passage, the crowd gives a loud cheer. That night, sitting on the stern rail beneath the stars, the boys experience a strange mixture of joy and sadness as they sail homeward, leaving the Pacific islands far behind.