The Council of Trent had already been in session for three years, when Charles V issued an edict known as the Interim, which forbade any change of religion until the council had finished its work; but at the same time he made concessions to the heretics which angered the Catholics both lay and clerical. Bobadilla was especially outspoken in the matter and in a public discourse was imprudent enough to condemn the imperial policy. Clearly he had not yet acquired the characteristic virtue of his great leader. Not only did he not mend matters by his intemperate eloquence, but he created an aversion for the Society in the mind of Charles V, which lasted till the time of St. Francis Borgia. Besides, he virtually blasted his own career. He was ordered to Naples by St. Ignatius and forbidden to present himself at the Jesuit house as he passed through Rome. He appears only once later and then in a manner scarcely redounding to his credit: objecting to the election of Laínez as vicar, although he had previously voted for him and obeyed him for a year. Happily the brilliant services of his fellow Jesuits who were at the Council of Trent and elsewhere, as well as his own splendid past, averted any very great damage to the Society.
Although Ignatius had been invited to be present at the sessions in Trent, he sedulously avoided the prominence which that would have given him personally; moreover, absence from his post as General of the newly-formed Institute would have materially interfered with the task of preparing successors to the great men who were already at work. Thus, Salmerón and Laínez were the Pope's theologians and Father Faber was summoned from his sick bed in Portugal to assist them, but he arrived in Rome only to die in the arms of Ignatius and never appeared at the council. Le Jay was present as theologian of the Cardinal Archbishop of Augsburg; Cavallino represented the Duke of Bavaria; and later Canisius and Polanco were added to the group. The coming of Canisius was due more or less to an accident. He had been laboring at Cologne to prevent the archbishop, Herman von Weid, from openly apostatizing; when the concessions to Melanchthon and Bucer had become too outrageous to be tolerated, he had hurried off to meet the emperor and King Ferdinand to ask for the deposition of the prelate. With the king he met Truchsess, the great Cardinal of Augsburg, and had no difficulty in gaining his point, but the Cardinal was so fascinated by the ability of the young pleader that he insisted on taking him to Trent as his theologian in spite of the protests of the whole city of Cologne.