The Church's primary aim in the 13th century was to assert papal authority and supremacy over secular rulers. Popes also called for reform throughout the entire Church and attempted to unify the Latin and Greek Churches. The unity of Christendom, the crusades against heretics and the recovery of the Holy Land from the Muslims were also priorities for the 13th century Church. Characteristic of this period was the Fourth Lateran Council of 1215, which set goals that the Church, led by the papacy, would strive to achieve for the next century. "Innocent III [1198-1216] himself summoned [the Fourth Lateran Council and advocated] the calling of a new crusade for the recovery of the Holy Land and the reform of the universal Church". Honorius III (1216-27) also dreamt of the recapture of the Holy Land and Church-wide reform. Likewise, Boniface VIII's (1294-1303) chief aims, even at the end of the century, were "the peace of Europe and the recovery of the Holy Land, were those of all preceding popes. He [defended] the unity of the Church and the supremacy of the ecclesiastical authority".
Pope Innocent III, the most powerful medieval Pope, imagined a united Christian society where the Pope obliged princes to rule with moral justice. Gregory IX (1227-41) even "planned the conversion of Asia and Africa". However, every Pope until the death of Emperor Frederick II were delayed in their plans because Frederick was unwilling to support many of the Church's goals. Honorius III "knew that without the co-operation of the emperor a successful crusade was impossible for the same reason he yielded to the emperor in many things which under different circumstances he would have strenuously opposed". He was also aware that "crusade was impossible as long as the Christian princes were at war with one another [therefore] he began his pontificate by striving to establish peace throughout Europe". Frederick's second excommunication by Gregory IX led to another feud between the empire and papacy. . "In 1249 [Innocent IV, 1243-54] ordered a crusade to be preached against Frederick II he continued to struggle against Conrad IV and Manfred [the emperor's sons] with unrelenting severity". Even after Frederick's death, Alexander IV (1254-61) made "futile efforts to unite the powers of the Christian world against the threatening invasion of the Tartars the unity of Christendom was a thing of the past".
Ever since the separation of the Western and Eastern Empires and their Churches, the Roman Church hoped that a reunion between the two was possible. Gregory IX temporarily restored the Syrian Monophysites to Catholicism, but was unable to unify the two Churches. Despite Gregory's efforts with the Greek Church, "the Greeks stubbornly adhered to their doctrine concerning the procession of the Holy Ghost and asserted that the Latins could not validly consecrate unleavened bread". After the conquest of Constantinople by Crusaders in 1204, "a Latin patriarch of Constantinople was appointed, and the Greek church was made subject to the Pope [which] exacerbated the hatred between Greek and Latin Christians". The Second Ecumenical Council of Lyons temporarily reunified the Churches but this fell apart in 1281 after the excommunication of Michael Palaeologus by Pope Martin IV (1281-85).
The 13th century showed a lazy, illiterate and corrupt clergy. The Fourth Lateran Council called for the "reform of the universal Church", and even outlawed all Church participation in customary barbarian judicial trials. "Honorius insisted that the clergy should receive a thorough training, especially in theology". Innocent III furthered the moral character of the priesthood and promoted (and enforced) celibacy; he reintroduced discipline to over-relaxed monasteries. One bishop's approbation was withheld because Honorius did not believe that he possessed sufficient knowledge; another bishop was deprived of his office when it was discovered that he was illiterate.
Although the Church was concerned with regaining the Holy Land, heretics were numerous within the lands of Christendom itself. Innocent III did not resort to the death penalty against the Manichean heretics, but preached a crusade against the Albigensians. Honorius III prepared crusades against the Moors (1218-19) and the pagan Prussians (1222). "Gregory IX was very severe against heretics decreed that all heretics and their abettors should be delivered to the nobles and magistrates for their due punishment, which, in case of obstinancy, was usually death". Gregory also started the papal inquisition and "approved of Emperor Frederick's law which decreed death by fire for unrepentant heretics".
The Teutonic Knights, founded in Germany in 1190, concerned itself with the forcible conversion of Slavs from 1226 onward.
Recovering the Holy Land was a priority for every Pope; whether a Crusade even happened was usually dependent on the capability and attitude of the Emperor. Frederick II was a royal annoyance to the Church when calling for Crusades. The Fourth Crusade (1202-04) had the lofty goal of liberating Jerusalem from the Arabs; however, many knights were paid off by Venetians with business interests, captured Constantinople, and established the Latin Empire. The Children's Crusade under Innocent III resulted in most of the participants being captured and sold as slaves, having never reached anywhere near Jerusalem. A general crusade was preached by both Innocent III and Honorius III for 1217, however, lack of unity among the Christian forces resulted in its failure. The Fifth Crusade under Honorius III was against Egypt and failed after some initial successes, while the Sixth Crusade captured Jerusalem before losing it permanently in 1244. The Crusades made no permanent reconquest of the Holy Land. They failed to put Islam's military advance in check and hastened the breakdown of the Eastern Empire. Finally, they distanced Latin Christians from both Greek Christians and Muslims. In conclusion, they were an absolute failure. The papacy, however, benefited from enhanced authority and prestige.
Innocent III was the most powerful medieval pope and held a lofty view of the papacy and its authority in secular affairs. Popes had four tools to use against problematic secular lords: interdict (prohibited all sacraments including baptism and matrimony), excommunication, deposition, and the ban (excommunication and deposition combined). Innocent III stated that the clergy were only subject to Church law, and not that of secular rulers. During a dispute for the German throne, Innocent issued the decretal Venerabilem, which stated that he had the right to decide between the two candidates. Innocent even declared the Magna Carta void because he felt it violated the rights of the king. When calling for the Fourth Lateran Council, "Innocent [had no] intention of allowing himself the humiliation of Lateran I where the council defeated the pope". Despite having both ecclesiastical and secular representatives at the council, "nothing was further from Innocent's mind than power-sharing". Since the Pope was thought to be Peter's successor, according to Innocent, he had authority over all the churches. In 1223, Honorius III safeguarded the Church in Bohemia against King Ottocar. In his bull Unam Sanctam, Boniface VIII declared that "all are subject to the Roman pontiff". Gregory believed that "the pope should be supreme ruler in Italy and by force of his spiritual authority over the whole Christian world the papacy should in all things hold the supremacy over the empire". In response to Frederick II's aggression, Gregory IX excommunicated him three times, placed him under the ban twice, and called a crusade against the emperor himself; he was not the only pontiff to take these measures against the stubborn emperor. However, after having excommunicated the emperor, Gregory was threatened by a mob in Rome and fled to Perugia in 1228. Only one of the German bishops published the Bull of excommunication. Gregory also tried to place Duke Otto of Brunswick on the throne while Frederick was crusading; he failed.
Despite being unsuccessful in large endeavors such as the Crusades, the 13th century Church was successful in its reforms and its inner crusades against heretics. Christendom was never united against outside forces, however, and the reunification of the East and Roman Churches was only temporary. Papal authority was asserted decisively by Innocent III, but those who succeeded him lacked the strength to keep control over problematic secular rulers, primarily Emperor Frederick II. Despite marking the decline of the papacy after Innocent III, the 13th century Church developed as a powerful institution.