Instead of attempting to proceed against the Jesuits on such discreditable evidence Pombal took the more effective ground that their moral principles, especially in regard to assassination, were the ultimate source of such outrages, and a very fierce controversy ensued. It seemed to become gradually plain to all that the long conflict of the Jesuits and their opponents was about to enter on its last stage. There were bishops who supported Pombal, and bishops who appealed to the Pope to check his progress. What Pombal mostly feared was the stirring of the ignorant and superstitious masses, and he proceeded with great caution. Before his project was realised in Portugal, the Jesuits of the colonies were on their way, under guard, to the mother-country, and, when they arrived, the Jesuit houses were surrounded by soldiers, the more active fathers were transferred to prison, and the rest were prevented from communicating with the laity. By the month of April 1759 about 1500 Jesuits were in jail or under guard. The King then informed the Pope that he was about to expel the fathers from his dominions. When Clement protested, stronger evidence of their intrigues was produced, and it is the general feeling of impartial contemporaries (like the English historian Coxe) and later authorities that some of these documents were forged. Clement still refused to sanction the expulsion, and a ruthless and indefensible step was taken by Pombal. On the feast of St. Ignatius (31st July) six Jesuits were condemned to be broken on the wheel, as if some value were now attributed to the evidence of a tortured witness.
This unjust sentence was not carried out, probably from a fear that the Pope would seriously question the jurisdiction of the civic authorities, but the plight of the Jesuits was lamentable. It was in Portugal that they had first attained power and wealth, and they had enjoyed an almost uninterrupted dominion for two centuries; now they lay on straw in the common jails, or tremblingly discussed the dark future in their overcrowded residences. On the first day of September the sentence of expulsion was enforced. The younger Jesuits were offered a dispensation from their vows by Cardinal Saldanha, but few accepted it, and the majority of them were put on ship and conveyed to the Pope's dominions. Pombal was cruel and unjust to the end in the realisation of his design; it is possible that he feared their later activity on foreign soil. There may be some exaggeration in the stories of their hardships, and indeed such a sentence could not be carried out without hardship, but one cannot defend his action in keeping 221 of the Jesuits in the jails of Portugal. One of them, Father Malagrida, an old man of seventy-two, seems to have been a little deranged by his imprisonment, and certain works which he wrote in prison were submitted to the Inquisition. He was condemned to be burned alive by the very tribunal which the Jesuits had been instrumental in establishing in Portugal. Of the 200 Jesuits, 88 died in jail, and the rest lingered in their humiliating captivity until the death of Joseph I. and dismissal of Pombal in 1777. By that time their Society had ceased to exist.