The historic animosity and struggle between the Pope and the Holy Roman Emperor is a famous one, a struggle that often included having the Emperor create a new Pope as a puppet, and the old Pope humiliating or excommunicating the Emperor.
With that said, the Protestant Reformation seemed like a near perfect out for the Emperors, no longer having their will being bent by Rome, they could answer to God alone. But, there was that 1 in a hundred chance that an Emperor who decided to be more friendly to Rome came to power, and as it happened the Pope-friendly Charles V came to the throne just in time for that to happen.
So, what would happen if the Emperor (or any other possible Emperor) had converted to Protestantism?