The problem is often from ignoring how the Pope interacts with the factions and how important his good favour can sometimes be. He's linked to the Papal States faction afterall, so mashing up his allies or making an enormous charitable donation for a new giant hat will work just the same as they do with any other faction. I make it a priority to get up a Theologians Guild and produce pious priests to replace the cardinals I'll have stabbed to death in their sleep. As a Catholic faction you have to accept excommunication or get stuck well into the battle for Papal favour.
When your reputation with the Pope totally sucks you can almost guarantee that any act of aggression against another Catholic faction will result in him demanding you stop the bloodshed against them....problem is that they might have good relations and have a varying but much larger number of turns to attack you before he finally gives them the same mission to cease hostility; and even worse, if they have good relations with the big hatted sod, they can just ignore that mission, and only lose some good favour instead of being excommunicated! On the other side of that equation though, the suicidally aggressive AI will cheerfully hurl itself into excommunication, allowing you to cheerfully walk into their lands to rape houses and burn women (am I getting that correct?).
Failing that, your only recourse is to use the superiority of your soft, squishy brain to prepare for an offensive more effectively, so multiple enemy cities can be taken in a single turn with the help of delicious siege engines. The Pope will then effectively be asking you to consolidate on your conquests and really make sure you've got a firm grip on all you've taken before moving on. Thanks Mister Big Hat, I'll be sure to do that.
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