After Francis had settled the business of the missions in India, he embarked in April, 1549, at the town of Cochin, intending to go to Japan by way of Malacca. He had with him a little band of friends, among whom were Father Cosmo Torres, Anger, now called Father Paul of Santa Fe, or the Holy Faith, and two or three Japanese students who had somehow found their way to the college at Goa. It was, of course, an immense help to him to have these young men to talk to for so many weeks. First they could teach him the Japanese language and the customs of the people, as well as their history and the two religions of the group of islands. Xavier was chiefly brought into contact with the one called Buddhism, taught five hundred years before Christ by a young Indian prince who lived near the Ganges, which had since spread over a large part of Asia. In the beginning, the founder, Gautama, or Buddha, had laid down strict rules of good living, but in the 2000 years which had passed since his death, his disciples had sadly fallen away from his teaching.

The governor of Malacca was a son of Vasco da Gama, the discoverer of the Cape of Good Hope, and he gave the missionaries everything that could be needed in their voyage, as well as handsome presents to the real  ruler of Japan. For ever since the twelfth century the power which for about 1800 years had been exercised by the dynasty of Jimmu, still represented by the present emperor or Mikado, had fallen into the hands of his minister and commander-in-chief, the Shogun. Till 1868, when the reigning Mikado suddenly broke his bonds, and adopted, to a great extent, European ways, he was merely a shadow; spoken of with awe and respect, it is true, and surrounded with luxury, but with no more power than the youngest of his subjects.

Before starting on the second part of his travels, Xavier was much cheered by letters from some of the Portuguese merchants in Japan, saying that they had spoken of the doctrines of Christianity to several people in the country who were well inclined to the faith, while a powerful noble (or Daimio, as the nobles are called) had sent an envoy to Goa to ask for teachers. The letter goes on to say that, when on landing the merchants had requested the Daimio of that district to appoint them a house where they might stay while they were doing their business, he had put a group of empty buildings at their disposal. The houses looked large and good, and the merchants rejoiced at getting such comfortable quarters—much better than anything they had expected. But in the night they were awakened by the cold—for it was still winter—and found that the warm blankets and quilts they had piled over them had slipped on to the floor. Pulling them up again, and tucking them in more securely, they went to sleep, but soon the same thing happened. Thus it was for many nights, till the poor, sleepy men began to think that some one was playing them tricks, though they could find nobody anywhere near the place. A few nights later they were all aroused by a frightful shriek, and seizing their swords they rushed to the room from which the sound proceeded, then occupied by a servant. But the door was bolted from inside, and in answer to their shouts, a voice inquired what was the matter.

That is for you  to tell us, cried the merchants; and when the man pulled aside the bolt they found him quite safe and the room empty.

We thought you were being murdered, they grumbled, and the servant replied:

No; but I woke feeling that some one was there, and on opening my eyes there was the most terrible spectre that ever I saw in my life. But in my fright I made the sign of the cross, and it vanished.

The next day, as the servant was nailing up crosses on all the doors, the neighbours who had heard the noise—for the houses were mostly of paper, on account of the great earthquakes—came running to know what it was the foreigners had seen.

Why should we have seen anything? answered one of the merchants who did not like being made game of, as he thought was the case. Then the Japanese told him that the house was haunted by an evil spirit—a kind of plague common in these parts—and that they wondered that the Christians had been able to bear its tricks for so long. Had they a charm that prevented them from being frightened? And if so, would the honourable gentlemen tell their servants what it was.

It was by this sign the spectre was conquered, replied the merchant, holding up a cross, and forthwith the Japanese set about making crosses of paper or wood and fixing them on to their houses. And from henceforth, ends the writer, the town was delivered from such ill-doings.

A voyage was always a terror to Francis, and he seems to have expected the one from Malacca to Japan to be more than usually full of danger. However, his fears did not prevent his holding long conversations with his Japanese pupils, and again expressing his surprise at their eagerness for knowledge. On his side, Xavier sends home accounts of the Japanese people and his reception at the city of Kagoshima, and his first impressions were very favourable. Of all nations I have ever seen, I cannot remember ever to have found any, Christian or heathen, so averse to theft, he writes. They are wonderfully inclined to all that is good and honest. Among barbarous nations there can be none with more natural goodness than the Japanese.

Perhaps he set too high a value on the interest  they showed in his preaching, for curiosity is a characteristic of every Japanese, but they listened to him eagerly, and for awhile it seemed indeed as if Christianity would displace the two old religions.

As has been said, the Jesuits were the great educational order of the church, and it was seldom that they opened a mission church without opening a school also. Their cleverest masters were given to the youngest pupils because they were more difficult to teach. Therefore, it was natural that Xavier should be struck with the number of colleges and the large university at Kioto or Miako where the Shogun lived, and the attention paid to the education of the boys who went to school at eight and stayed there till they were twenty, after which wives were found for them. The love of children for which Xavier was always noted made him notice with pleasure the care taken of the funny little black-haired things, tumbling about in their loose dresses, and crowing with delight at the wonderful masses of flowers that springtime brought. He soon made friends with them and taught them their catechism, and his heart was full of high hopes for their future. Little did he think, when he left Japan to return to India, that some of his small playfellows would be called upon to lay down their lives for their faith.

It was, as was natural, the bonzes or Buddhist priests who first stirred up strife, and persuaded one of the Daimios near Kagoshima, to forbid any of his people to become Christian on pain of death. In spite of this edict, however, for some months they were left alone, and Francis and his followers went about from one island to another teaching and preaching as usual. The very journeys were full of difficulties which would have been impossibilities to most men. A civil war had broken out, and bands of soldiers were to be met with all over the country. The peasants insulted the missionaries and often threw stones at them. Snow lay deep, and on one occasion the missionaries lost their way in a forest. The sun was hidden in the clouds and they had nothing to guide them, and it seemed as if they must spend the night where they were, and would probably be found frozen to death next morning. While they were in this plight, a horseman came up, burdened by a box which threatened every moment to slip to the ground. He stopped when he saw the little band, and asked how they came there. They told him that they did not know in what direction they ought to go, on which he laughed roughly, and said:

Let this man carry my luggage and follow me, and you will find yourselves by and by at the end of the forest.

Thankfully Francis laid the box on his shoulders, and started off rapidly, as he dared not lose sight of the horse. So fast did he go that his companions were soon left behind, and when, many hours later, led by the tracks of both man and horse, they emerged into a plain with a small town on it, they found Xavier lying exhausted on a bank, his feet and legs so badly bruised and swollen that they were obliged to carry him to an inn, and let him rest for many days before he could proceed on his journey.

The history of the mission to Japan is a history of contrasts. The Shogun, the Daimios, and the people seem to have been anxious to adopt Christianity, and nothing could have been more splendid than the reception given to Xavier at this time at Miako. Almost unexampled honours were showered upon him; he was seated at the Shogun's table, and went daily to see him and to talk to him about his religion. More than one bonze had been converted, which made the rest more bitter than ever; and all his experiences told Francis that everything was ripe for persecution. The lives of the Christians only depended on the good will of the various rulers, and especially of the Shogun; and who could tell how long that might last?

It was, therefore, with very mixed feelings that he received letters, bidding him return to India at once with the Portuguese trading fleet. He had never meant to do more than spend a couple of years in Japan, so as to organise the different missions, and the two years were now up. Yet the promising beginning had given place to dark fears for the future, and it was very hard to leave his converts when danger was so close at hand. But obedience was his first duty, and for the rest he must trust in God. So he went over to Bongo for the last time to rebuke the prince for his evil life, and, as usual, his words did not fail of their effect at the moment. Still he did not feel confident; the Japanese he knew, were easily moved—in either direction.

In November 1551 Xavier sailed for India, having written beforehand to request that other missionaries might be sent to Japan, as the work and constant travelling was too much for the few fathers. In answer to his appeal, Father Balthazar Gago, and some other priests, embarked for Miako, and, after a kind welcome from the Shogun, went on to the port of Amanguchi, across the mountains, where Father Torres awaited them. The two priests were not long together: Balthazar departed to the district allotted to him, and a month later, on the outbreak of a civil war, Torres was literally forced by the converts to put himself out of danger by leaving for Bongo, which was at present at peace.

Things remained much in this state for the next five years. The missionaries never faltered in preaching and teaching, and thousands allowed themselves to be baptised. The fathers rejoiced greatly, but at the same time they knew well that in this fact lay their peril. Was it likely that the bonzes would stand tamely by and watch their power slipping way? Twice or thrice they had already stirred up their followers to revolt and it did not need a very wise head to tell that on the next occasion the struggle would be more serious.

The opportunity of the bonzes came at last in Firando, when the Portuguese priests were commanded by the prince to quit the town, and for the sake of their converts they dared not disobey. Their departure was the signal for a general riot, when the churches were sacked and the altars were pulled down—no doubt with the assistance of the Buddhist children! But vain were the threats or persuasions of the bonzes; the converts stood firm, and even the execution of a slave-woman had no power to move the rest. Japanese, unlike many Europeans, are never afraid to die.

The persecution once begun, spread rapidly. The fathers who had escaped from Firando were caught by some Japanese, stripped and turned loose, though their lives were spared. For days they remained hidden in a cave, without food or light, till, with the help of some friends, they managed to reach Bongo. Here they went about from city to city, and even founded three hospitals in which they gathered the sick, the foundling babies, and the lepers. As before, the prince was on their side, and offered them money, and when they refused this for themselves, he gave it at their request, for the support of the hospitals.

In accordance with the changes that were so strong a feature of the Japanese mission, affairs now began to take a turn for the better. The most powerful man in Japan took the Christians under his protection, and though he did not himself become one, a Daimio was converted and was baptised by the name of Bartholomew. A cross was embroidered on his robes, which of itself was an act of courage, for death on the cross was reserved, as was the case in Rome, for the lowest felons. Thus proclaiming his faith he rode at the head of his troops during the war, and surrounded the city temple. The soldiers occupied the position unsuspiciously, for it was their custom, before marching to battle, to pray for success to the war god, but it is strange to learn that they obeyed their prince without a word when he ordered them to break down the image of Buddha. After the peace was made, he destroyed the other temples in his dominions, and even, one is sorry to hear, interfered with the harmless custom of spreading out a feast once a year to the dead relatives of the people.

Now, reverence for their ancestors is one of the most cherished beliefs of the Japanese, and they arose as one man against this insult. It was to no purpose that Bartholomew gave the money which the feast would have cost to feed the poor. He had touched them in their tenderest place, and they would not forget it. The rebellion burst forth. Bartholomew, after escaping once, was besieged in his huge stone mountain fortress, but though he got the better of them on that occasion his action had dealt a severe blow to the Christian religion.

The year 1582 marks a stage in the history of Japan, for it was the date of the interesting embassy sent to the Pope, Gregory XIII., by some of the most powerful princes to ask for more help in Christianising the country. The ambassadors themselves were unusual also, for they were four young Daimios, all under sixteen. They set out under the charge of two Jesuit fathers, and after spending some time in Goa went on to Lisbon and Madrid. Everywhere they were received with the utmost kindness, and were shown all that the capitals held of wonder and magnificence, and we may be sure that the sights were keenly appreciated by their young eyes and quick brains. As soon as they entered Italy, crowds turned out to see them, curious to know what these strangers from the ends of the earth would look like, and how they would behave. They only saw four slight, pale-faced, rather short boys, quiet, but not in the least shy, managing with perfect ease the horses sent for them. Their dress alone would have marked them out as different from Europeans. Their white silk, wide-sleeved robes were covered with birds and flowers, all beautifully worked in their natural colours, and kept in place by a folded sash, and their finely tempered swords had their sheaths and hilts covered with precious stones and enamelled designs. In this guise they followed the carriages of the Spanish, French, and Venetian ambassadors, and, surrounded by the Roman nobles, they rode through the city for their audience of the Pope. When they left Rome, after witnessing the coronation of the new Pope, Sixtus V., it was as Knights of the Order of the Golden Spur, and under the promise to maintain the Christian religion with the last drop of their blood.

The persecution, which had for so long been smouldering, was destined to come to a head under the famous Hideyoshi the Shogun, the conqueror—with the help of an army largely composed of Christians—of the kingdom of Corea. Perhaps if the Jesuits had been left to manage by themselves, peace might have existed for some time longer, but a body of Franciscan missionaries came over from the Philippine Islands, and their zeal was greater than their discretion. By their tactless conduct in thrusting their religion openly in the face of the people of Nagasaki, the most prosperous missionary settlement in the country, they drew on themselves a sentence of banishment. The Jesuits, out of their long experience, implored them to be more careful, and pointed out that the future of the Catholic Church was at stake; and the arrival of the new bishop appointed by the Pope, a man of sense called Martinez, smoothed things over with the Shogun for a short time. Then, stories reached Hideyoshi's ears that the Franciscans were again transgressing the orders he had given, and he began to suspect a deep-laid plot to destroy his government. This idea was fostered when he learned that a Spanish captain had been heard to say that Philip II owed his wide possessions chiefly to the missionaries.

That silly and imprudent speech was the death-knell of the Christians in Japan.

The first thing to be done was to discover exactly who were Christians, and so papers were prepared and the Christians ordered to come and sign their names. One and all—even the children—obeyed, though they understood fully that the object of this census was to be able to find them at once in case the persecution was decided on. But at this moment, Hideyoshi only intended the Franciscans to die; the Jesuits, as a body, he liked and wished to spare as long as he had an excuse for doing so.

A huge multitude was gathered on the plain of Nagasaki to see the sentence carried out. The martyrs were led out altogether, the Franciscan friars, two or three Jesuits who had attended their church, and several young children. The punishment was the same for them all—crucifixion, but in Japan that death, though only suffered by those who are considered degraded, was more merciful perhaps than any other. The victims were only tied to the crosses and were killed by one thrust of a sword.

Thus died the martyrs, scorning alike the prayers of their relatives and the offers of pardon made by the governors if they would give up this new faith and apostatise.

The death of Hideyoshi afforded the Christians a short breathing space, but under his successor (who usurped the place of Hideyoshi's son) the many edicts which were in force against them, Jesuits as well as Franciscans, were carried out or not, just as it pleased the various princes.

In Higo large numbers were driven from their houses, and anyone who sheltered them incurred the penalty of death. At the end of six months, however, the few survivors were allowed to take refuge with their fellow Christians.

Thankful they were to be permitted to rest for a little with the kind Jesuits, though they were greatly saddened by the news that a fresh edict had been proclaimed in Higo, summoning Christians, on pain of death, to be present at a ceremony which was to be performed on a certain day in the house of a bonze. The governor was ordered to see that the edict was carried out, and it was understood that those who obeyed should be considered to have returned to the Buddhist religion, and be pardoned. The governor did his utmost to persuade two nobles—John and Simon—his own personal friends, to comply with the order, hoping that the others might follow their example, but it was in vain that he urged them to bribe the bonze to say they had apostatised, or to allow the ceremony to take place in private, so that none might know. Neither John nor Simon would listen to his proposals, and when, in pursuance of his duty, the governor was obliged to suffer John to be brought before the bonze, and the Buddhist book was placed by force upon his head, he proclaimed his faith so loudly that it was impossible to prevent the punishment being executed at once.

With Simon he fared no better. The young man was with his mother when the governor entered, and he entreated the poor lady to induce her son not to throw his life away. But the mother, herself a Christian, declared it was an honour that Simon should die for his Lord; and the governor, angry and sorrowful, left the house, sending, as was the custom, a friend of both himself and Simon to behead the condemned man. This friend, Jotivava, was joyfully received by Simon, who begged his mother to fetch warm water, as if it was a feast, that he might wash himself. This done, he walked between his wife and his mother to the great hall, followed by three Christian brothers and the noble sent to be his executioner. He died, praying to God for mercy, and twenty-four hours after, his wife and his mother died likewise.

From all parts of the country news poured in of hundreds and thousands who had fallen victims to their religion, and among these many were children. A story is told of a whole Christian family who were condemned in the province of Arima. The father and uncle were put to death first, but there was a short delay in the execution of the grandmother and the two little boys. Your father has died for Christ, and so must you, she said to them when she received the message. Is there anything better that could happen to us? answered they. When is it to be? Now, she replied. Go and bid farewell to your mother. The boys left her, and arranged with their nurses how their toys should be given away among their friends; and they put on the white garments which their grandmother had prepared for this day that she knew would come. Then they went in to their mother.

Farewell, dear mother, they said, kneeling; we are going to be martyred.

Oh! if I could only be with you, she cried, for she and her daughter had escaped condemnation, but your father is holding out his arms to receive you. Kneel down, loosen your collars, bow your heads, and call Jesus! Mercy.  As she spoke the soldiers entered, and, taking the children from her, carried them to the palanquin where their grandmother awaited them.

Happy were those who suffered death from the sword, for soon the martyrs passed through fire and other horrible tortures from this life to another. At length, in 1614, it was resolved to banish the Christians from the kingdom, but out of all the four orders at that time working in Japan—for the Dominicans and Augustinians now had missions there—the Jesuits alone were allowed to say a farewell mass at Miako. Then they were sent to Nagasaki, whence they embarked for their different places of exile.

The massacres went on for many years longer, and at last there was hardly a Christian left in Japan. Then all the ports, except Nagasaki and Firando, were closed to foreigners, and the country remained a sealed book till the Mikado, in 1868, resolved to make it as free as the Western World.