We all know this prophecy from St. Francis (said to have been given shortly before his death):
So we have here a prophecy about a man who's not canonically elected (vs. a "true Sovereign Pontiff"), who will be not a Pastor but a destroyer.

I know there are some Bennyvacantists here who apply this to Bergoglio, but some time ago I made a connection in my mind between this prophecy and the prophecies of St. Malachy.

After Pius XII died, the next pope in line had the label of "Pastor et Nauta" ("Pastor/Shepherd and Sailor") applied by the St. Malachy prophecy.  I heard the story of a rumor circulating at the time of this election that Cardinal Spellman hired a boat, put sheep on it, and sailed down the Tiber (in an attempt to conform to this prophecy).  That could have been a satirical jab against the ambitions of the Cardinal, but it's a side issue anyway.

What if St. Francis' prophecy was pinpointing the exact Antipope he's referring to here, since while St. Malachy refers to a "Pastor et Nauta", St. Francis said that he won't be a true Pastor (but a destroyer).  This would refer to Roncalli not having been canonically elected due to the Cardinal Siri situation.

Just a thought/musing I wanted to throw out there.

Prophecies of St. Malachy

Concerning Ireland

This prophecy, which is distinct from the prophecies attributed to St. Malachy concerning the popes, is to the effect that his beloved native isle would undergo at the hands of England oppression, persecution, and calamities of every kind, during a week of centuries; but that she would preserve her fidelity to God and to His Church amidst all her trials. At the end of seven centuries she would be delivered from her oppressors (or oppressions), who in their turn would be subjected to dreadful chastisements, and Catholic Ireland would be instrumental in bringing back the British nation to that Divine Faith which Protestant England had, during three hundred years, so rudely endeavoured to wrest from her. This prophecy is said to have been copied by the learned Dom Mabillon from an ancient manuscript preserved at Clairvaux, and transmitted by him to the martyred successor of Oliver Plunkett.

Concerning the Popes

The most famous and best known prophecies about the popes are those attributed to St. Malachy. In 1139 he went to Rome to give an account of the affairs of his diocese to the pope, Innocent II, who promised him two palliums for the metropolitan Sees of Armagh and Cashel. While at Rome, he received (according to the Abbé Cucherat) the strange vision of the future wherein was unfolded before his mind the long list of illustrious pontiffs who were to rule the Church until the end of time. The same author tells us that St. Malachy gave his manuscript to Innocent II to console him in the midst of his tribulations, and that the docuмent remained unknown in the Roman Archives until its discovery in 1590 (Cucherat, "Proph. de la succession des papes", ch. xv). They were first published by Arnold de Wyon, and ever since there has been much discussion as to whether they are genuine predictions of St. Malachy or forgeries. The silence of 400 years on the part of so many learned authors who had written about the popes, and the silence of St. Bernard especially, who wrote the "Life of St. Malachy", is a strong argument against their authenticity, but it is not conclusive if we adopt Cucherat's theory that they were hidden in the Archives during those 400 years.

These short prophetical announcements, in number 112, indicate some noticeable trait of all future popes from Celestine II, who was elected in the year 1143, until the end of the world. They are enunciated under mystical titles. Those who have undertaken to interpret and explain these symbolical prophecies have succeeded in discovering some trait, allusion, point, or similitude in their application to the individual popes, either as to their country, their name, their coat of arms or insignia, their birth-place, their talent or learning, the title of their cardinalate, the dignities which they held etc. For example, the prophecy concerning Urban VIII is Lilium et Rosa (the lily and the rose); he was a native of Florence and on the arms of Florence figured a fleur-de-lis; he had three bees emblazoned on his escutcheon, and the bees gather honey from the lilies and roses. Again, the name accords often with some remarkable and rare circuмstance in the pope's career; thus Peregrinus apostolicus (pilgrim pope), which designates Pius VI, appears to be verified by his journey when pope into Germany, by his long career as pope, and by his expatriation from Rome at the end of his pontificate. Those who have lived and followed the course of events in an intelligent manner during the pontificates of Pius IX, Leo XIII, and Pius X cannot fail to be impressed with the titles given to each by the prophecies of St. Malachy and their wonderful appropriateness: Crux de Cruce (Cross from a Cross) Pius IX; Lumen in caelo (Light in the Sky) Leo XIII; Ignis ardens (Burning Fire) Pius X. There is something more than coincidence in the designations given to these three popes so many hundred years before their time. We need not have recourse either to the family names, armorial bearings or cardinalatial titles, to see the fitness of their designations as given in the prophecies. The afflictions and crosses of Pius IX were more than fell to the lot of his predecessors; and the more aggravating of these crosses were brought on by the House of Savoy whose emblem was a cross. Leo XIII was a veritable luminary of the papacy. The present pope is truly a burning fire of zeal for the restoration of all things to Christ.

The last of these prophecies concerns the end of the world and is as follows: "In the final persecution of the Holy Roman Church there will reign Peter the Roman, who will feed his flock amid many tribulations, after which the seven-hilled city will be destroyed and the dreadful Judge will judge the people. The End." It has been noticed concerning Petrus Romanus, who according to St. Malachy's list is to be the last pope, that the prophecy does not say that no popes will intervene between him and his predecessor designated Gloria olivæ. It merely says that he is to be the last, so that we may suppose as many popes as we please before "Peter the Roman". Cornelius a Lapide refers to this prophecy in his commentary "On the Gospel of St. John" (C. xvi) and "On the Apocalypse" (cc. xvii-xx), and he endeavours to calculate according to it the remaining years of time.

Regarding St. Malachy's prophecy, we only need to count the Popes, taking as our starting point one Pope in the list that is not in doubt, like Celestine II. If we do that, we should be able to recognize BXVI being the last with a 'nickname" in the list, "the glory of the olive." The Peter the Roman part at the end is something to do with the Holy Pope/Great Monarch prophecy. That is my take on it anyway.