It's not even the main story arc, and of course, Rodrigo Borgia is the worst Pope in history and generally an evil dude, but everything else -- the descriptions of buildings, groups, locations, etc. Every character associated with the Church in the game is an evil bad guy, corrupt or incompetent. I'm not Catholic, but I studied Church history and there was a point, about 50% of the way through Assassins Creed 2, where it went from mildly historic with an ax to grind, to just .. anti-historic sensationalist nonsense that felt like it was written by a 16-year-old who is pissed that their parents made them go to private school. I've heard it explained that the reason all of the history bits and descriptions read like they're written by a 14-year-old Conor Oberst is because they're supposed to be from that angsty guy who follows Desmond around, but it still doesn't fly.