His brilliant and extraordinary life was marred, indeed stifled, by continuing battle with the papacy. 

His father, Heinrich VI, despite opposition of Pope Celestine III, had married Constance of Sicily, daughter and heir-presumptive of Roger II of Sicily. In 1191 the pope crowned Heinrich VI and Constance Emperor and Empress. Heinrich VI then set out to recover Sicily which had been divided by the feudal barons who had elected Tancred, an illegitimate grandson of Roger II, as king. Only by treacherously massacring many of the Sicilian aristocracy was Heinrich VI able to 
succeed. 
In 1194, at the age of forty, Constance gave birth to her only child, the future Emperor Friedrich II. In 1197 Heinrich VI died before he was able to inflict any further cruelties, leaving Constance 
as regent to deal with the German soldiers of fortune. However, Constance was capable and determined, securing the support of Pope Innocent III who, in the summer of 1198, crowned both Constance and her infant son. Sadly, Constance died on 27 November 1198 and Friedrich II became the ward of the pope while rival factions in Sicily fought for control. 
Friedrich II was ignored and would have starved had the poorer citizens of Palermo not taken pity and looked after him. At the age of seven he was kidnapped. Fortunately, however, his kidnapper died a few months later, otherwise Friedrich II might have been blinded and castrated, as had been Tancred's son by orders of Friedrich II's father. 
After this he led a wild life with grooms and huntsmen which taught him how ordinary people lived. He studied languages, including Arabic, and was widely read. In his learning he was encouraged by Papal legates and Muslims alike. The Norman kings had made Sicily the most cultivated court in Europe, from which Friedrich II now benefitted. 
At fourteen, he was declared to be of age and the pope selected a wife for him, Constanza of Aragon, who was considerably older and the widow of King Emmerich of Hungary. Constanza both improved his manners and gave birth to a son, Heinrich, in 1211. 
Friedrich II's right to succeed his father as Emperor had been ignored and, at the age of seventeen, he had to prepare himself for a possible invasion by Emperor Otto IV. However, the Guelf princes, in favour of the House of Hohenstaufen, deposed Otto and elected Friedrich II as Emperor. Then, at the age of eighteen, he was invited to come to Germany as Emperor-elect. 
He would have been happier had he remained in Sicily but he accepted the call as destiny and went to Germany. However, Pope Innocent III insisted that he first come to Rome to pay homage. As 
well he was expected to give Sicily to his baby son as Innocent III did not want to have Friedrich II as both Emperor in the north of Rome and King of Sicily in the south. Friedrich II had other ideas but was wise enough  not to reveal them. 
Although Friedrich II found a hostile Germany, by diplomacy he overcame all opposition and was crowned with various titles. Yet he still had to be crowned by the pope to be confirmed as emperor. Although he did not care for Germany, he still had his wife and son come there and even had his son elected as his successor without consent of the pope. 
However, Pope Innocent III had been succeeded by the gentle Pope Honorius who, after a promised crusade to liberate Jerusalem, crowned Friedrich II in Rome on 22 November 1220. Friedrich II then went straight to Sicily and issued laws based on earlier Norman laws which 
had made Sicily the most prosperous kingdom in Europe. Also, the army and fleet were built up. 

Friedrich II had to have his kingdom in order before he could set out on the crusade, and he needed time to make Sicily prosper in order to finance the crusading venture. He built ships especially to 
transport two thousand knights and ten thousand soldiers. Part of each ship could be let down so that the knights could disembark already mounted and ready to meet the enemy. Also he had to defeat the Muslim population of Western Sicily, after which he settled them as farmers in Apulia. 

While preparing himself for the crusade, on 23 June 1222, his wife Constanza died, and on 9 November 1225, as a second wife he took Yolande de Brienne, daughter of Jean de Brienne, King of Jerusalem. 
She gave him his second legitimate son, Konrad IV in 1228 and died thirteen days later. In 1227 Pope Honorius died to be succeeded by Gregory IX who was to become Friedrich II's formidable adversary. After seven years Friedrich II set out to go on crusade; but after three days at sea, an epidemic broke out and he decided to return while the others went on, as he preferred to recover in Sicily rather than die at sea. Pope Gregory IX then excommunicated him as he considered this to be just another excuse for not going on crusade. 
When the excommunication became known, the whole army of forty thousand knights and soldiers returned from the Holy Land. Europe then watched to see whether the pope would again be 
victorious in the struggle for supreme power between the pope and the emperor. Friedrich II tried in vain to appease the pope as he wanted to make the crusade once he had recovered. Despite further troubles caused by the pope, he set out for Jerusalem which greatly annoyed the pope. 

No-one expected any success as he arrived with a much less impressive army than originally intended. However, for some considerable time he had been on friendly terms with the Sultan of 
Egypt and, through diplomacy, Friedrich II succeeded where armies had failed. In a treaty in 1229, those parts of Jerusalem considered holy by the Christians were returned to them, while those regarded holy by the Muslims were retained by them. In the Church of the Holy Sepulchre, Friedrich II crowned himself King of Jerusalem as the Pope's Patriarch would have nothing to do with the ceremony. 
Friedrich II then returned to Sicily in glory. The Pope, embarrassed and distrustful, forced Friedrich II to make many concessions; but in August 1230 the excommunication was lifted. Pope 
Gregory IX disliked the remarkable Constitutions of Melfi, which had been drawn up by jurists. These included the schools for training civil servants and doctors but, most importantly, that all were equal for the law, taking away the jurisdiction of prelates and nobles. Even though Friedrich II was an autocrat, he found nothing more odious than the oppression of the poor by the rich. 

The Pope was distrustful of Friedrich II's sophistication and curiosity as Friedrich II's court was full of learned men and poets. Also, not only has Friedrich II's own book on "The Art of Hunting with Birds" remained a classic, but he had important works translated from Arabic. He also built castles in Apulia. At the same time he believed in cleanliness to the extent that his daily baths were regarded a scandal. 
Having been a widower for seven years, in July 1235, he married again, this time to Isabella, daughter of John Lackland, King of England. By Isabella he became the father of a son and a daughter. 
Isabella died in 1241 and from then on he remained unmarried. During his life he also fathered at least eleven illegitimate children. To retain his influence in Germany, he needed to secure lines of 
communications which had to be via the papal state and Lombardy. The pope prevented Friedrich II from uniting northern Italy by which action Friedrich II suspected the pope of encouraging insurrection against the Empire. When he eventually realized that the opposition of the pope was continual, Friedrich II tried to deprive him from temporal power. 
For a second time Gregory IX then excommunicated Friedrich II in 1239, but the kings of England, France and Hungary sent forces to help Friedrich II in his struggle against the Lombard League. The nearly hundred-years-old Gregory IX then verbally attacked Friedrich II for many sins, mostly invented; so Friedrich II decided to capture both Rome and the pope who had been deserted by many of his cardinals. However, Gregory IX inspired the Romans to defend their city and Friedrich II decided to withdraw his forces. Twice more he advanced and withdrew. After the first time, Gregory IX had died and been replaced by Innocent IV who escaped dressed as a soldier. 
In 1245 in Lyons, Innocent IV declared Friedrich II to be deposed, which undermined the latter's position. Friedrich II then had to depose his own son for incompetence as well as for allying himself with Friedrich II's enemies. In February 1249 he failed to capture Parma which kept his main route across the Appenines closed. Various attempts on his life were made, ordered by the pope, till eventually he died in 1250 and was buried in Palermo.

Source: Leo van de Pas