He suggested that Rome itself, "once the center of true faith", could become the seat of the apostate system, fulfilling the prophecy of a fallen "mother church" that gives rise to many false religious daughters. He pins the blame on infiltration from Satanic Masons, basically. He takes it oh so far but perhaps doesn't even realize that what he has discovered as being a mere potential is in fact the ONLY real-world vector for such a system as described in Revelation to be established via.

In the very act of warning about the Catholic church transforming into Mystery Babylon he testifies to it being the ONLY CANDIDATE ON EARTH who could be it in the first place!

edit- Re reading even this comment leads me to have much more to say. Malachi was mistaken in his timeline. He failed to see that what he feared had already happened long ago, and he was retroactively realizing it and ascribing its current state into the potential future; but it had already been Mystery Babylon, and was, and still is. Cognative dissonance is powerful, but God is greater. Through HisStory we can see more clearly than those who lived to carry it forward.