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In the meanwhile, says Palou, "that fervent zeal which continually glowed and burned in the heart of our venerable Father Junipero, did not permit him to forget the principal object of his journey." As soon as Portolà had left the encampment, he began to busy himself with the problem of the mission which, it had been determined, should be founded on that spot. Ground was carefully chosen with an eye to the requirements, not only of the mission itself, but also of the pueblo, or village, which in course of time would almost certainly grow up about it; and on the 16th of July - the day upon which, as the anniversary of a great victory over the Moors in 1212, the Spanish church solemnly celebrated the Triumph of the Holy Cross - the first mission of Upper California was dedicated to San Diego de Alcalà, after whom the bay had been named by Sebastian Viscaino, the explorer, many years before. The ceremonies were a repetition of those which had been employed in the founding of the Mission of San Fernando at Villicatà; the site was blessed and sprinkled with holy water; a great cross reared, facing the harbour; the mass celebrated; the Venite Creator Spiritus sung. And, as before, where the proper accessories failed, Father Junipero and his colleagues fell back undeterred upon the means which Heaven had actually put at their disposal. The constant firing of the troops supplied the lack of musical instruments, and the smoke of the powder was accepted as a substitute for incense. Father Palou's brief and unadorned description will not prove altogether wanting in impressiveness for those who in imagination can conjure up a picture of the curious, yet dramatic scene.
The preliminary work of foundation thus accomplished, Father Junipero gathered about him the few healthy men who could be spared from the tending of their sick comrades and routine duties, and with their help erected a few rude huts, one of which was immediately consecrated as a temporary chapel. So far as his own people were concerned, the padre's labours were for the most part of a grievous character, for, during the first few months, the records tell us, disease made such fearful ravages among the soldiers, sailors and servants, that ere long the number of persons at this settlement had been reduced to twenty. But the tragedy of these poor nameless fellows - (it was Junipero's pious hope that they might all be named in Heaven) - after all hardly forms part of our proper story. The father's real work was to lie among the native Indians, and it is with his failures and successes in this direction that the main interest of our California mission annals is connected.
They were not an attractive people, these "gentiles" of a country which to the newcomers must itself have seemed an outer garden of Paradise; and Junipero's first attempts to gain their good will met with very slight encouragement. During the ceremonies attendant upon the foundation and dedication of the mission, they had stood round in silent wonder, and now they showed themselves responsive to the strangers' advances to the extent of receiving whatever presents were offered, provided the gift was not in the form of anything to eat. The Spaniards' food they would not even touch, apparently regarding it as the cause of the dire sickness of the troops. And this, in the long run, remarks Palou, was without doubt "singularly providential," owing to the rapid depletion of the stores. Ignorance of the Indians' language, of course, added seriously to the father's difficulties in approaching them, and presently their thefts of cloth, for the possession of which they developed a perfect passion, and other depredations, rendered them exceedingly troublesome. Acts of violence became more and more common, and by-and-bye, a determined and organized attack upon the mission, in which the assailants many times outnumbered their opponents, led to a pitched battle, and the death of one of the Spanish servants. This was the crisis; for, happily, like a thunderstorm, the disturbance, which seemed so threatening of future ill, cleared the air, at any rate for a time; and the kindness with which the Spaniards treated their wounded foes evidently touched the savage heart. Little by little a few Indians here and there began to frequent the mission; and with the hearty welcome accorded them their numbers soon increased. Among them there happened to be a boy, of some fifteen years of age, who showed himself more tractable than his fellows, and whom Father Junipero determined to use as an instrument for his purpose. When the lad had picked up a smattering of Spanish, the padre sent him to his people with the promise that if he were allowed to bring back one of the children, the youngster should not only by baptism be made a Christian, but should also (and here the good father descended to a bribe) be tricked out like the Spaniards themselves, in handsome clothes. A few days later, a "gentile," followed by a large crowd, appeared with a child in his arms, and the padre, filled with unutterable joy, at once threw a piece of cloth over it, and called upon one of the soldiers to stand godfather to this first infant of Christ. But, alas! just as he was preparing to sprinkle the holy water, the natives snatched the child from him, and made off with it (and the cloth) to their own ranchería. The soldiers who stood round as witnesses were furious at this insult, and, left to themselves, would have inflicted summary punishment upon the offenders. But the good father pacified them, attributing his failure - of which he was wont to speak tearfully to the end of his life - to his own sins and unworthiness. However, this first experience in convert-making was fortunately not prophetic, for though it is true that many months elapsed before a single neophyte was gained for the mission, and though more serious troubles were still to come, in the course of the next few years a number of the aborigines, both children and adults, were baptized.
 The mission was transferred in 1874 from the location selected by Junipero to a site some two miles distant, up the river.