Fray Ignacio de Sanctivañes, the first archbishop of Manila arrived by the same ships, in May 1598, but he died of dysentery in August of that year.

On December 14, 1600, a Spanish fleet under the command of Doctor Antonio de Morga fought two Dutch pirate ships at Cavite.

After nine months at sea, after many of the men had died and much of the merchandise had been thrown overboard, the San Geronimo put back to the Philippines, off the islands of Catenduanes, outside of the channel of Espiritu Santo, and there was wrecked, although the crew was saved.

The flagship "Sancta Margarita, after the death of the general and most of the crew, ported at the Ladrones Islands (Guam) and anchored at Zarpana.

He confirmed the peace and friendship with the chiefs and people of Tampacan and Lumaguan, restored and set in better order the Spanish settlement and fort, and began to make preparation for the war against Buhahayen.

He wrote to inform Governor Tello that it would be better to withdraw the camp from Mindanao River, so that it might not perish; and that a presidio could be established on the same island in the port of La Caldera, which could be left fortified, in order not to abandon this enterprise entirely, and so that their friends of Tampacan and Lumaguan might be kept hostile to the people of Buhahayen.

He was ordered first to make a great effort to chastise the enemy in Buhahayen, and then to burn the Spanish settlement and fort and go to La Caldera, fortify it, and leave there a sufficient garrison with artillery, boats, and provisions for its maintenance and service.

As soon as possible after this, the Spaniards attacked the settlements and forts of Buhahayen which such effect that the enemy, seeing themselves hard pressed and without anyone to help them, sent proposals of peace to Ronquillo.

The Spanish abandoned and burned their base on Mindanao River and left for Manila, leaving only a garrison of 100 soldiers at La Caldera.

The governor sent to arrest General Ronquillo on the road before he entered Manila, intending to proceed against him by law for having withdrawn the camp and army from Mindanao River without awaiting the orders he should have expected after the favorable turn of affairs.

Some Dominican missionaries in Cagayan persuaded Governor Tello that Magalat should be pardoned, after knowing their condition for the revolt, and the latter fulfilled the favor.

After Magalat was released, he went back to Cagayan and still continued to incite the people to fight, and many Spaniards and loyal natives were murdered by the rebels.

[1] In 1596, the galleon San Felipe laden with Philippine goods sailed for New Spain, but because of severe weather it was forced to land in Japan, in territory controlled by Toyotomi Hideyoshi.

Fray Pedro Baptista, superior of the Franciscan religious residing in Miako (Kyoto), attempted to mediate with the authorities, but without success.

Their right ears were cut off, and they were paraded through the streets of Miako and through those of the cities of Fugimen, Usaca, and Sacai, to the great grief and sorrow of all Christians who saw their sufferings.

[1] The Spaniards of the San Felipe eventually made it back to Manila, in various Japanese and Portuguese ships, but with a total loss of the merchandise they carried.

Governor Tello sent an ambassador to Hideyoshi bearing gifts (including an elephant) and also a protest at the treatment of the religious and the sailors, and a demand for the return of the goods the San Felipe had been carrying.