When John died, and Luisa became Regent for her young son, the angry nobles made a vigorous effort to dislodge the Jesuits. John's elder son, who had had a Jesuit tutor, had refused to marry, and had wished to join the Society. Men recalled the earlier King Sebastian, and said that the Jesuits were attempting to seize the crown. The Jesuit-tutor was even accused of betraying the military secrets of the country; and one of his colleagues, Father Vieira, was so badly compromised by a letter of his which was intercepted that John had been compelled to make a foreign ambassador of him; another Jesuit was the diplomatic representative of Portugal at Rome. The nobles resented this situation; but Fernandez was in too strong a position, and the rule of the Jesuits continued under the Regency. Fernandez died, however, in 1660, and it is a second Jesuit of that name (as is sometimes forgotten) who took a leading part in the extraordinary events of the year 1668.
The elder prince, Theodose, had died prematurely, and Alphonso succeeded to the throne. Whether there was some incurably morbid strain in the youth, or whether the Jesuit tuition had made him incapable of serious political life, we cannot say; but, as he grew to manhood, Alphonso VI. entered upon ways of violence and licence which recall the youth of Nero. His court was filled with the wild companions of his orgies, and he paraded his vices on the streets and in the taverns of his capital. He exchanged his Jesuit confessor for a Benedictine monk, snatched the reins from the hands of his mother, and threatened to drag the country very speedily into the abyss which awaited it. Sober nobles and statesmen looked on with alarm, and it was inevitable that a conspiracy to dethrone him should shortly arise. But the details of the revolution, in which the Jesuits were very active, reflect little honour on its actors.
Alphonso had married Marie Isabelle de Savoie-Nemours, whose Jesuit confessor, Father de Ville, listened sympathetically to the story of the outrages she endured. Father de Ville and his colleagues were not less sympathetic when Marie Isabelle transferred her affection to the King's handsome young brother, Dom Pedro, and they entered into a plot to replace Alphonso by Pedro. The chief plotter seems to have been Father Vieira, whom the French historian regards as the glory of the Portuguese Province at that time. Vieira was not without ability, but he was a turbulent and meddlesome politician, and so eccentric in his religious ideas that he fell into the prison of the Inquisition. The Jesuits secretly engaged the nobles in a plan to dethrone and divorce Alphonso and replace him by his brother. Divorce is, of course, unknown to the Catholic Church, but it has never failed to discover a flaw in a marriage which it was expedient to undo, and, with something very like levity or cynicism, the Jesuits and the Queen determined to accuse the King of impotence and get the marriage annulled: a king who was notorious for his amours and had had a child by one of his mistresses. Pedro was then informed of the Queen's amiable disposition and the support of the nobles, and the conspiracy began.