So there are many reasons that led the church to grow into conflict with the Hohenstaufen most of them were actually caused by the numerous wars waged by the previous popes against the holy Roman emperor and king of Sicily, Frederick II.

One of the first reasons was Frederick behavior with the muslim which was one of tolerance and goodwill, as Frederick just like his Normans  predecessor loved to surround himself with  Muslim knowledgeable men.

The main reason that sparked the first war was the fact that Frederick II went crusading and instead of conquering Jerusalem through force he preferred to use diplomacy. We have many Muslim sources that describe the emperor as a pleasant and knowledge-hungry monarch that during his stay in the sultan's palace tested, the sultan's courtiers with mathematical and philosophical problems . In the end the treaty of Jaffa was signed, since the sultan was currently in a civil war against his brothers and Frederick II had many internal problems mainly rebellious vassals back at home as such he wanted to speed up the process. Under the terms of the treaty, Frederick received Jaffa, Tripoli, Nazareth, and Jerusalem, though Jerusalem's walls were to be taken down and a 10-year truce was to be  signed. 

Frederick then returned home where he wa excommunicated by the pope for going hand to hand with the Muslims, and there the first papal war against Frederick came to be . 

A war that led the way for other wars between the successor popes and Frederick.Then after Frederick's death, the pope would continue in their hostility with the kings of Sicily culminating in the call of Charles of Anjou and his coronation as the new king of Sicily which sparked the start of the novel after the battle of Benevento, where Manfred, the uncle that usurped the main character of his kingdom, was defeated and killed.

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By the way start of the novel is slow because mc needed to start from scratch for his first campaign, warfare basically start at 56, so if you really can't bear some slow development, such as acquiring loans, ally and weapons skip to chap. 56 .