It was not until 1756 that the resistance of the natives in the Jesuit reductions was finally overcome, and the proofs (which we will see later) of secret Jesuit provocation deeply impressed the King. There was at that time on the papal throne a Pope who had repeatedly condemned the Jesuits. We shall see later that their behaviour on the Chinese and Indian missions was, in a different way, as irregular as their behaviour in South America, and Benedict XIV. severely condemned them. His chief minister, Cardinal Passionei, was also opposed to the Jesuits. King Joseph now submitted to the Vatican an account of the conduct of the Jesuits in South America and asked that they should be reformed. Meantime, in the autumn of 1757, Pombal persuaded the King that the Jesuits were fomenting disorder in Portugal itself, and an order was signed for the expulsion of all Jesuit confessors from the court. In the night of 19th-20th September the servants and soldiers entered the palace, and Fathers Moreira, Costa, and Oliviera awoke to find themselves sentenced to removal from their comfortable offices. Pombal then ordered that no Jesuit should be allowed to approach the court, sent a very forcible justification of the King's conduct to the other European courts, and pressed the demand for reform at Rome.
On 1st April 1758 the Pope signed the decree for an inquiry into the behaviour of the Jesuits, and Cardinal Saldanha was sent to South America to conduct the inquiry. The proceedings at Rome had been kept secret from the Jesuits until the decree was signed, and Pombal's agents had secured the appointment of a cardinal who was no friend of the Society. But both the Pope and the General died in the spring of that year, and, when Cardinal Saldanha justly reported that the Jesuits of South America had been wrongly engaged in commerce, the new General, Ricci, appealed to the new Pope, Clement XIII., who was known to be favourable to the Society. Clement appointed a commission of inquiry which, being composed of friends of the Society and making no investigation on the spot, declared the Jesuits innocent.
The declaration was absurd and insincere, as we shall appreciate when we come to examine the conduct of the Jesuits on the missions, and Pombal saw that he must deal with the fathers in Portugal. In June (1758) the cardinal-patriarch had laid an interdict on all the Jesuits in the diocese of Lisbon, and public opinion seemed to be prepared for a drastic step. An event that occurred in the night of 3rd-4th September of that year gave Pombal his opportunity. As the King returned from the house of his mistress, the Marchioness Tavora, several shots were fired at him, and a large number of members of the Tavora family were arrested and put to the torture. One of the prisoners, the Duke d'Aveiro, said, under torture, that the Jesuits were privy to the conspiracy, and eight of the leading fathers were arrested and tortured. The duke afterwards retracted, and it must be said that, beyond this worthless declaration, there is no positive evidence to connect the Jesuits with the outrage, though they had been in close correspondence with the Tavoras. They were, however, not punished on that ground with the other prisoners. Only one of the Jesuits was executed, but for heresy, not treason; the others were kept in prison, while all the Tavoras were executed.