If involved in this 'mess' with the US, the US military can take him into custody as an unlawful combatant IAW LOAC. Unless the Vatican declared war on the US and we didn't hear about it. Then he'd be a POW.
There are other options when it comes to the Pope besides arrest.
It depends on whether or not Trump wants to take down or save the Catholic Church, which I humbly submit may be more Melania’s call than his, since she is Catholic and he was raised Presbyterian.
If they want to save the Church and its reputation, they will force Francis and some of the cardinals out. Maybe they secretly arrest them. Maybe they cut a deal and disappear them to some island nation where they will live out their lives in some sort of “nice” prison— basically being free to come and go in a village but under an assumed identity while the world thinks they died of Covid or something.
But then perhaps Trump and or Melanie believe saving the Catholic Church requires exposing the corruption even if it results in the Church shrinking considerably in size as people leave and check out the Greek Orthodox church, the Lutherans, or something else.