Breath of Fir... no. Xenos... no. Final Fan... no. That other Final Fan... no. Still another Final Fan... no.
Um. Wild Arms 3... *spoilers* not sure if you want to call him a pope, but the head of the religion is a good guy. Unfortunately the divine guidance he is receiving is still coming from the main villain, so as good a person as he is he does end up furthering some bad things. Sad that this is the closest I can think of.
Tales of the Abyss... kinda works but when you say "pope", the old evil dude pops into my head before the young altruistic dude, even though the latter is technically the head of the religious order.
Oh well. I generally loves me my evil pope characters anyway.
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