Archbishop McCloskey took part in the Second Plenary Council of Baltimore, in 1866, whose acts are such a code of doctrine and discipline. "Of it he was a burning and a shining light," said Archbishop Gibbons. "He was conspicuous alike for his eloquence in the pulpit, and for his wisdom in the council chamber. I well remember the discourse he delivered at the opening session. The clear, silvery tones of his voice, the grace of his gestures and manner, the persuasive eloquence and charm of his words are indelibly imprinted on my memory and imagination. Just before ascending the pulpit, a telegram was handed to him, announcing the destruction by fire of his Cathedral. He did not betray the slightest emotion, notwithstanding the sudden and calamitous news. Next morning I expressed to him my surprise at his imperturbable manner. "The damage," he replied, "is done, and I cannot undo it. We must calmly submit to the will of Providence.""
The decrees of the Plenary Council, with those of the Council of New York, were promulgated by him in a Synod held by him at New York, in September, 1868.
The next year he was summoned to attend a General Council at Rome, the first held in the church since the Synod of Trent. The Council of the Vatican had been equalled by but few in the number of bishops, by none in the universality of the representation. Before modern science had facilitated modes of travel and communication, the area including those who attended was comparatively limited. To the Vatican Council, however, they came not from all parts of Europe only, but from Palestine, India and China; from the Moslem States of Africa; the European colonies; the negro kingdoms of the interior; America sent her bishops from Canada and the United States; the Spanish republics, Australia and the islands of the Pacific even had their bishops seated beside those of the most ancient Sees. Here Archbishop McCloskey was a conspicuous figure, respected for learning, experience, the firmness with which he held the opinion he mildly but conclusively advanced. In the committee on discipline his wisdom excited the highest admiration of the presiding cardinal.
When the impious seizure of Rome made the sovereign Pontiff a prisoner in the Vatican, the proceedings of the council were deferred to better days, which the Church still prayfully awaits. Archbishop McCloskey returned to his diocese; but the malaria of the Campagna had affected his health, never rugged, and shattered some years previously by a railroad accident, on a journey required by his high office. But he resumed his accustomed duties, inspiring good works, or guiding and supporting them like the Catholic Protectory, the Catholic Union of New York, and its branch since developed to such wide-reaching influence, the Xavier Union.