Java, 1942. Captain Yonoi and Sergeant Hara run a Japanese prisoner-of-war camp containing 600 Allied soldiers. They ignore the higher-ranking Hicksley in favour of bilingual Colonel John Lawrence, the only prisoner who understands Japanese culture.

In a courtroom in nearby Batavia, Major Jack Celliers is questioned by Yonoi. He claims that he was beaten when interrogated, and removes his shirt when challenged - to Yonoi's discomfiture. Celliers is taken before a firing squad - who deliberately miss him (on Yonoi's orders).

Lawrence and Hara discuss the alleged rape of a Dutch prisoner, De Jong, by Kanemoto, a guard. Hara asks if all Englishmen are homosexuals, and claims a true samurai would not be afraid of homosexuality. Lawrence says that war creates intense bonds between men, but not necessarily homosexual ones.

Celliers arrives at the camp, and Yonoi tells Hara that he wants him in good health. Lawrence asks him why he's so interested, but Yonoi turns to Hicksley and asks how many POWs are experts in armaments. Hicksley refuses to tell him.

That night, Hara visits Lawrence and asks him about Celliers. Lawrence says that he's a born leader. Hara says that he'd admire him more if he committed suicide out of shame. Lawrence says that being a prisoner is one of the fortunes of war: suicide is the coward's way out. Hara says he's not afraid of dying - at twelve, he offered his life to the Emperor.

After Kanemoto is forced to commit hara-kiri, a horrified De Jong swallows his tongue and chokes to death. A furious exchange between Hicksley and Yonoi, leads to prisoners being denied food for 48 hours. Celliers gathers red flowers, laying them on De Jong's bed. For this, he is beaten and thrown in the cells.

Celliers survives an assassination attempt by Yonoi's butler, but is confronted by Yonoi as he tries to escape. They draw knives, but Celliers plunges his into the ground. Yonoi says that if he defeats him, he will be free - but they are interrupted by the arrival of Hara and his men.

Yonoi tells Lawrence that he has been sentenced to death for smuggling a radio. Yonoi says he'll be dying on his behalf. Lawrence angrily says that he'll die, but not for Yonoi. Cursing the Japanese gods, he desecrates an altar.

Lawrence shares a cell with Celliers, who asks him what's wrong with the Japanese. Lawrence says they're a nation of anxious people who went mad en masse - but he doesn't hate any individual Japanese. He tells Celliers about a dream involving a mysterious encounter with a woman in Singapore.

Celliers recalls two incidents involving his brother, an angelic blond boy who loved to sing. In one, he is chided for disobeying Celliers by seeking help following a confrontation with other boys. In the other, Celliers does nothing as his brother is subjected to a humiliating initiation ritual at school. As a result, he never sang another note, Haunted by this, Celliers joined the army in order to do something positive.

Lawrence and Celliers are taken to a makeshift courtroom in front of a drunk Hara, who orders them to be freed, and wishes Lawrence a merry Christmas (in English).

A furious Yonoi orders all prisoners on parade - regardless of health. Even when one collapses, Yonoi brusquely repeats his question about armaments experts. Hicksley says there aren't any. Yonoi sentences him to death, and draws his sword. Celliers walks over to Yonoi and kisses him on both cheeks. Yonoi raises his sword, then faints.

Later, a new captain denounces Yonoi and says that he will not be so sentimental. Celliers is buried up to his neck in the ground. That evening, the men sing within earshot of Celliers, who is dreaming of a reconciliation with his brother. Yonoi cuts a lock of Celliers' hair, and bows before him. A butterfly lands on the dead Celliers' forehead.

In 1946, Lawrence visits Hara in his cell on the eve of his execution, and finds him prepared to die - the victim of men who think they're right, just as Lawrence had been four years earlier. After reminiscing, Hara wishes Lawrence a merry Christmas.