The samurai, Nishi, and their retainers arrive at the port of Tsukinoura, in the northeast of Japan. They stay in a temple, where they are ordered to remain until the Council of Elders is assembled. Three days later, Lord Tsumura, one of the elder statesmen, comes to the temple to question them. His enquiries make it very clear that Christianity is now regarded with great hostility in Japan. The samurai and Nishi are both angered by Lord Tsumura’s declaration that the change in circumstances has rendered their long, arduous journey useless, and Nishi impulsively exclaims that he has converted to Christianity.

The samurai admits to Lord Tsumura that he, too, has become a Christian, but he says that neither of them was sincere; they converted for the good of the mission. Nonetheless, they are both interrogated and forced to write recantations before being sent home. The samurai returns to his former life of hard work on the land. Eventually, Lord Ishida summons him to his mansion. Unlike Lord Tsumura, Lord Ishida is sympathetic to the samurai’s plight. However, he says that the samurai must be very careful not to attract attention now, since anyone suspected of Christian sympathies is subject to harsh penalties. Hasekura will receive no thanks for his service and is fortunate to keep his lands and his life.

Soon after returning home, the samurai opens the box in which he has stored various mementoes of his journey, including scraps of paper with prayers and Bible verses written on them, given to him by priests and monks in the monasteries where he stayed. He burns these scraps of paper, in case they should be used against him if he is ever charged with being a Christian. As he thinks of the former monk he met in Mexico, he feels sympathy with his worship of the miserable, emaciated figure of Christ, a man who understood suffering.

One day, when speaking to Yozo, the samurai sees a resemblance between his old retainer and Jesus Christ. He asks Yozo if he believes in Christianity, and Yozo says that he does. Hasekura advises him to keep quiet about it. There is a strong unspoken sympathy between the two men, and Hasekura feels that Yozo understands him better than anyone else.

After a year in the Philippines, Velasco returns to Japan. He admits that this is a reckless course of action but points out that Christ was equally reckless in his journey to Jerusalem. When he arrives in Japan, he pretends to be a merchant but is immediately suspected and put in jail with other Christians. Following interrogation, he is taken to Nagasaki to await judgment from the magistrate there. Velasco and his fellow Christians are kept in disgusting conditions so that some of them fall sick and die even as they wait to be executed.

The samurai receives orders, delivered by the officers of Lord Ishida, that he is to be punished for his conversion to Christianity by being confined to his estate. After delivering this message, one of the officers tells him that this punishment, more than a year after his return, is connected to the arrival of Velasco in Japan. Later, Lord Ishida summons the samurai to his mansion. He professes to sympathize with his plight, telling him that his fate is not his own fault but the outcome of political machinations beyond his control. Ishida does not specify what is to happen to the samurai but ominously declares that he will look after his son.

The story ends with Velasco being burned at the stake, after he repents of his arrogance and dishonesty, and sees that he has confused God’s will with his own. Immediately before his death, he learns that the samurai and Nishi have also been executed for their conversion to Christianity.