[B.T.]

I have not voted, yet.

If JP II. is the pope in the Twilight war, we should take in account, that he was the Pope, that travelled the most. In Wikipedia is an article on his travels.
Some of these travels might not have the same destination as IRL! In the later half of the 90ies the Pope visited severals states in the former Eastern Bloc - I don't think this had happened in T2k. But he would have been travelling to other States/countries.
Depending on his location (Choose your destination of the Popes "tour"!) he might stay at that place, when things get dense in Europe - Brazil is not unlikely (Dragoon mentioned Brazil before!).
If the Pope is in Europe, I can imagine, he'd like to stay in Rome, but leaves for an uncertain ammount of time to get back there, if the situation is more stable.

I think, France is not a bad destination - there had been Popes residing in Avignon (I don't remember who said in in the "People of Poland"-threat, but although some of the anti-Popes spent their time in Avignon, there had also been "official" Popes in Avignon!).
Switzerland is an option, another place in Italy is another one.
Still another country come to my mind: Ireland! It has a catholic population and it is not that likely as an aim for nukes!
If the Pope sees his new residence as a place of a temporary exile, he could stay allmost anywhere!

The idea of a SpecFor team trying to capture the Pope is a nice one. Maybe I'll have a try on this, too.

Edit: It was "Adm. Lee" in No. 35 of the "People of Poland" who mentioned Avignon as being not likely. Just in case someone was asking!