I don't have the guide for how to step by step, but mostly, you have to be nice to them.
This is from one of the Devs. 3 years ago, so some of it might be incorrect due to changes during an update.
ending 2 (the happy ending) visit the church anytime. mention the place is rundown.. then visit again after 12 hours, from 17:00 to 20:59. ask about the pope. visit again the day after. choose to help. visit again the next day. tell FF to go to the Vatican.