[6] His mission was to aid Don Juan in the pacification of the Spanish Netherlands, which was the property of the Crown of Spain, to stop the advance of Protestantism, and to prepare in secret the expedition for the conquest of England.

[11] In Spring 1582, Bishop Sega was back in his diocese, but on 20 September 1583, he received a letter from Cardinal Guastavillani, appointing him to another mission to Spain.

He was to attempt to get King Philip II to revive the league with Venice and the Papacy against the Turks; he was to revive Gregory XIII's enterprise against England; he was to persuade the King to support Prince Ernest of Bavaria, who had been chosen Archbishop of Cologne but who was being resisted by the schismatic heretic Otto von Truchses and Prince Casimir.

[12] On 24 November 1583 the Spanish response was given by Cardinal de Granvelle: the league was refused; the King was committed to the English expedition, but circumstance were unfavorable at the time; the Catholics of Cologne were being supported by the Prince of Parma, to the extent that his commitments in the Netherlands made it possible, but in any case, the Elector Ernest would have to pay the expenses, since the King could not.

Bishop Sega left the Spanish court at the end of January 1584, but fell ill at Barcelona, and did not arrive in Italy until June.

The assignment of the "Monsignori Riformatori" was to carry out an official visitation of all the churches and colleges in Rome; each member of the clergy who held a benefice of any kind was summoned to give an account of himself.

The new papal legate a latere was Cardinal Enrico Caetani, and he was accompanied by Bishop Filippo Sega with the title of Nuncio.

[20] Due to his service in France, he was not assigned a titular church until his return, when, on 5 December 1594, he received the red hat and became the Cardinal-Priest of Sant'Onofrio.