The President and Auditors having arrived at the Philippines in the month of May 1584, whilst Diego Ronquillo was governing, Dr. Santiago de Vera entered upon the government, and immediately founded the High Court, and the seal was received and placed with all solemnity and festivities that were possible. They then began to attend to business, both of justice and in matters of war and administration, with great profit to the country. During this time fresh succours continued to be sent to the Moluccas, and for the conquest of the island of Terrenate, which the captain-major of Tidore desired to make: Captain Pedro Sarmiento went from Manila for this purpose, and on another occasion the captain and sergeant-major Juan de Moron, but neither of these expeditions met with the desired result.

The President Santiago de Vera also continued to carry out the pacification of some provinces of the islands, and effected several matters that in all respects were most fitting. He discovered a rebellion and insurrection which the principal natives of Manila and Panpanga were proposing to carry into effect against the Spaniards, and justice was done upon the guilty. He built with stone the fortress of Our Lady of Guidance within the city of Manila on the land side, and he caused some artillery to be founded for arming it, by means of an old Indian named Pandapira, a native of Panpanga: he and his sons rendered this service for many years afterwards, until they died.