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While Junipero and his companions were thus engaged in planting the faith among the Indians of San Diego, Portolà's expedition was meeting with unexpected trials and disappointments. The harbour of Monterey had been discovered and described by Viscaino at the beginning of the seventeenth century, and it seemed no very difficult matter to reach it by way of the coast. But either the charts misled them, or their own calculations erred, or the appearance of the landscape was strangely deceptive - at any rate, for whatever reason or combination of reasons, the exploring party passed the harbour without recognizing it, though actually lingering awhile on the sand hills overlooking the bay. Half persuaded in their bewilderment that some great catastrophe must, since Viscaino's observations, have obliterated the port altogether, they pressed northward another forty leagues, and little dreaming of the importance attaching to their wanderings, crossed the Coast range, and looked down thence over the Santa Clara valley and the "immense arm" of San Francisco Bay. By this time the rainy season had set in, and convinced as they now were that they must, through some oversight or ill-chance, have missed the object of their quest, they determined to retrace their steps, and institute another and more thorough search. On again reaching the neighborhood of Monterey, they spent a whole fortnight in systematic exploration, but still, strangely enough, without discovering "any indication or landmark" of the harbour. Baffled and disheartened, therefore, the leaders resolved to abandon the enterprise. They then erected two large wooden crosses as memorials of their visit, and cutting on one of these the words - "Dig at the foot of this and you will find a writing" - buried there a brief narrative of their experiences. This is reproduced in the diary of Father Crespé; and its closing words have a touch of simple pathos: "At last, undeceived, and despairing of finding it [the harbour] after so many efforts, sufferings and labours, and having left of all our provisions but fourteen small sacks of flour, our expedition leaves this place to-day for San Diego; I beg of Almighty God to guide it, and for thee, voyager, that His divine providence may lead thee to the harbour of salvation. Done in this Bay of Pinos, the 9th of December, 1769." On the cross on the other side of Point Pinos was cut with a razor this legend: - "The land expedition returned to San Diego for want of provisions, this 9th day of December, 1769."
The little party - or more correctly speaking - what was left of it, did not reach San Diego till the 25th of the following month, having in their march down suffered terribly from hunger, exposure, wet, fatigue and sickness. Depressed themselves, they found nothing to encourage them in the mission and camp, where death had played havoc among those they had left behind them six months before, and where the provisions were so fast running low that only the timely reappearance of the San Antonio, long overdue, would save the survivors from actual starvation. Perhaps it is hardly surprising that, under these circumstances, Portolà's courage should have failed him, and that he should have decided upon a return to Mexico. He caused an inventory of all available provisions to be taken, and calculating that, with strict economy, and setting aside what would be required for the journey back to San Fernando, they might last till somewhat beyond the middle of March, he gave out that unless the San Antonio should arrive by the 20th of that month, he should on that day abandon San Diego, and start south. But if the governor imagined for a moment that he could persuade the padre presidente to fall in with this arrangement, he did not know his man. Junipero firmly believed, despite the failure of Portolà's expedition, that the harbour of Monterey still existed, and might be found; he even interested Vicente Vila in a plan of his own for reaching it by sea; and he furthermore made up his mind that, come what might, nothing should ever induce him to turn his back upon his work. Then a wonderful thing happened. On the 19th of March - the very day before that fixed by the governor for his departure, and when everything was in readiness for to-morrow's march - the sail of a ship appeared far out at sea; and though the vessel presently disappeared towards the northwest, it returned four days later and proved to be none other than the San Antonio, bearing the much needed succour. She had passed up towards Monterey in the expectation of finding the larger body of settlers there, and had only put back to San Diego when unexpectedly, (and as it seemed, providentially), she had run short of water. It was inevitable that Father Junipero should see in this series of happenings the very hand of God - the more so as the day of relief chanced to be the festival of St. Joseph, who, as we have noted, was the patron of the mission enterprise.
The arrival of the San Antonio put an entirely new complexion upon affairs; and, relieved of immediate anxiety, Portolà now resolved upon a second expedition in quest of Monterey. Two divisions, one for sea, the other for land, were accordingly made ready; the former, which included Junipero, started in the San Antonio, on the 16th of April; the latter, under the leadership of Portolà, a day later. Strong adverse winds interfered with the vessel, which did not make Monterey for a month and a half. The land-party, following the coast, reached the more southern of the great wooden crosses on the 24th of May, and after some difficulty succeeded at last in identifying the harbour. Seven days later, steering by the fires lighted for her guidance along the shore, the San Antonio came safely into port; and formal possession of the bay and surrounding country was presently taken in the name of church and King. This was on the 3rd of June, the Feast of Pentecost; and on that day of peculiar significance in the apostolic history of the church, the second of the Upper California missions came into being. Palou has left us a full account of the ceremonies. Governor, soldiers and priests gathered together on the beach, on the spot where, in 1603, the Carmelite fathers who had accompanied Viscaino, had celebrated the mass. An altar was improvised and bells rung; and then, in alb and stole, the father-president invoked the aid of the Holy Ghost, solemnly chanted the Venite Creator Spiritus; blessed and raised a great cross; "to put to flight all the infernal enemies;" and sprinkled with holy water the beach and adjoining fields. Mass was then sung; Father Junipero preached a sermon; again the roar of cannon and muskets took the place of instrumental music; and the function was concluded with the Te Deum. Though now commonly called Carmelo, or Carmel, from the river across which it looks, and which has thus lent it a memory of the first Christian explorers on the spot, this mission is properly known by the name of San Carlos Borromeo, Cardinal-Archbishop of Milan. A few huts enclosed by a palisade, and forming the germ at once of the religious and of the military settlement, were hastily erected. But the actual building of the mission was not begun until the summer of 1771
 The Diary, furnishing a detailed itinerary of the expedition, is given in full in Palou's noticias de la Nueva California.