Worked out some of the gameplay.
You begin as a protestant church (two lucky players will randomly become the papacy and the patriarchate of constantinople) based in a single province. Each monastery in a province is Catholic or Orthodox and provides Religious Points to the pope and patriarch respectively. You gain Religious Points(RP) from each province you are present in. If you spread far enough in a country to become the state church, you may enact a series of reforms and gain RP from every province in that country. One of which is to abolish the monasteries in the nation, at which point the pope or patriarch only get RP from provinces they are in. Another is to break any and all communion with the pope or patriarch, an expensive reform that cause the persecution of catholicism in the nation. You may also declare war on catholic, orthodox, or other protestant nations to force-convert their provinces.
The pope and the patriarch can fight back by converting provinces back, rebuilding monasteries, declaring holy wars, and generally being a pain in the arse to the reformed churches. No matter what the Tsar and the Holy Roman Emporer will remain loyal to their respective churches. The pope and patriarch may also declare a crusade to take the holy land back from the muslims, a major supplier of RP. They may also undertake in costly reforms to eliminate corruption(which detracts from RP),earn better relations with the protestants, and make it harder for their provinces to be converted.
The holy land will serve as a sort of king of the hill setting. Once the holy land is taken by one of the two churches, reformed churches can move in and Ottoman armies will periodically appear to reclaim their land. Another option will then be available to raze mecca(off-map), providing a great deal of RP and provoking the Ottoman empire to recieve several armies each turn in their holy jihaad against all the states that hold whatever church destroyed Mecca. The holy land will come under constant attack and very well might be lost. If the ottoman nation is driven off the map, a mission becomes available to dethrone the caliph and forever end the muslim threat. This will be one of the victory conditions of the game.