The points of attack were the alleged gift of prophecy, the public invectives against Rome which brought the Papacy into contempt, "and the artifices by which the separation of the Tuscan Congregation had been obtained. Savonarola defended himself point by point with great ability. He excused himself from visiting Rome on the plea of weak health, which was forcing him to abandon the pulpit, and of the danger from Milanese assassins on the road. He submitted his doctrines to the judgment of the Church, referring the Pope to his Compendium Revelationum for his defence of prophecy; his Holiness, he constantly repeated, had been deceived by the slanders of his enemies. Alexander vacillated; he was pressed on the one side by Ludovico il Moro and the Friar's Florentine enemies, on the other by the government and by the several Florentine envoys, all personally devoted to Savonarola. He was perhaps genuinely unwilling to take a decisive step against one whose holiness he respected; for sinners are not unable to value saints. In September, 1495, he adopted an obvious method of removing the Dominican from Florence by re-uniting the Tuscan to the Lombard Congregation. In answer to Savonarola's remonstrances he abandoned this intention, but in November, 1496, he ordered the union of all the Tuscan Dominican convents under a new Tusco-Roman Congregation. Even this brief contained no patent evidence of hostility. The papal consent to the independence of the Tuscan Congregation had been won almost by a trick; the Congregation had not proved an entire success, owing to the resistance of the larger Tuscan towns; even the union of the convent at Prato had only just been effected, and not without difficulty. The smallness of the Congregation virtually confined Savonarola's ministrations to Florence, which was most unusual. No previous hostility existed between the Roman and Tuscan Dominicans, like that which animated the latter against their Brethren of Lombardy; the new Vicar-General, the General, and the Protector of the Order were all of them Savonarola's friends. The Roman authorities might reasonably have doubted whether his temporary withdrawal from the city would prove an unmixed evil, either for Florence or for himself.
To this brief Savonarola's reply from the pulpit was almost a declaration of war. For he hinted not obscurely, that there were limits to obedience; that if a brief of excommunication were brought into the city on a spear-head he should know how to reply; and that his answer would make many a face turn pale. His Apology of the Brethren of San Marco was a formal appeal from the Pope to the public. Yet of Savonarola's resistance Alexander took little notice, until he felt assured that there were signs of a reaction within Florence. Then, he launched his brief of excommunication, which was solemnly read between lighted torches in the Florentine churches on the evening of June 18, 1497. To the clauses of the brief which condemned Savonarola for disobedience in not visiting Rome and for doctrinal heterodoxy, he could readily reply