On the surface, the popes appear to have been in a good position in the late thirteenth century.

Frederick II was defeated, and imperial pressure on Rome was relieved. (See also Chapter 8.) Louis IX, the French monarch, was a zealous supporter of the church, as seen by his two catastrophic Crusades, which earned him sainthood.

Although it only lasted seven years, the Council of Lyons declared a reunification of the Eastern church with Rome in 1274, when the Western church took advantage of Byzantine emperor Michael VII Palaeologus' (r. 1261–1282) plea for help against the Turks. Despite these encouraging developments, the church's situation was not as good as it looked.

There were foreboding indications as early as Pope Innocent III's papacy (r. 1198–1216), when papal power was at its peak. Innocent had developed the theory of papal plenitude of power and used it to make saints, dispose of benefices, and establish a centralized papal monarchy with a clearly political agenda.

Innocent's elevation of the papacy into a powerful secular authority spiritually harmed the church while strengthening it politically. Following that, the church as a papal monarchy became further estranged from the church as the "body of the faithful."

Until the Protestant Reformation, both reformers and heretics protested in the name of the "true Christian church" against this supposed "papal church."

What Innocent started, his successors improved.

The papacy established its own law court, the Rota Romana, during Urban IV (r. 1261–1264), which regulated and consolidated the church's legal operations. The system of clerical taxation was refined in the later part of the thirteenth century; what began in the twelfth century as an emergency expedient to obtain finances for the Crusades became a permanent institution.

During the same time period, the papal authority to appoint to numerous important and minor ecclesiastical offices—the "reserve of benefices"—was substantially expanded. The pope became a strong political entity in the thirteenth century, regulated by its own law and tribunals, supported by an efficient international bureaucracy, and focused with secular interests.

The centralization of the church by the Pope weakened both diocesan power and public support.

The centralization of the church by the Pope weakened both diocesan power and public support. Rome's interests grew to dominate church appointments, rules, and discipline, rather than local requirements. Lower clergy who were dissatisfied with the discipline of local bishops petitioned Rome's superior authority.

Bishops and abbots denounced such undermining of their power in the second part of the thirteenth century. To its detractors, the Roman church was little more than a licensed, "fiscalized," bureaucratic entity. As early as the late twelfth century, heretical organizations such as the Cathars and Waldensians invoked the biblical ideal of simplicity and detachment from the world.

Other church-loyal reformers, such as Saint Francis of Assisi, spoke out against perceived materialism in official religion.

Internal theological strife was not the only thing eroding the thirteenth-century church. Because of the fall of imperial power, the pope in Rome was no longer the voice of anti-imperial (Guelf, or propapal) feeling in Italy.

Instead of being the focal point of Italian opposition to the emperor, popes found themselves on the defensive against their former friends. That was the ironic cost of the papacy's victory over the Hohenstaufens.

Rulers with a vested interest in Italian politics redirected the intrigue that had previously targeted the emperor to the College of Cardinals. For example, Charles of Anjou, the French king of Naples and Sicily (r. 1266–1285), was successful in establishing a French-Sicilian group inside the college. Such efforts to exert control over the college's judgments caused Pope Gregory X (r) to resign.

In 1294, following a more than two-year impasse, such a conclave picked a holy but incompetent hermit as Pope Celestine V. Celestine abdicated after only a few weeks in office, under mysterious circumstances.

He, too, died under mysterious circumstances; his successor's detractors later claimed that the powers behind the papal throne assassinated him to secure the continuation of the papal office.

The Cardinals were startled by Celestine's tragicomic rule and elected his opposite, Pope Boniface VIII (r. 1294–1303), a nobleman and adept politician. His papacy, on the other hand, would mark the beginning of the demise of papal claims to great power status.

The Royal Assault on Papal Authority When Boniface became Pope in 1294, France and England were on the verge of war. Only Edward I's preoccupation with Scottish insurrection, which the French fostered, kept him from invading France and launching the Hundred Years' War a half-century sooner than it did.

As both governments prepared for war, they taxed the clergy severely under the guise of preparing for a Crusade. Pope Innocent III ordered in 1215 that the clergy were not to pay taxes to monarchs without the approval of the Pope. Boniface strongly opposed English and French clergy taxes, seeing it as an infringement on established clerical privileges. On February 5, 1296, he issued a bull called Clericis laicos.

In England, Edward I replied by denying the clergy the ability to be heard in royal court, thereby stripping them of the king's protection. But Philip the Fair retaliated with a vengeance: in August 1296, he prohibited the shipment of money from France to Rome, depriving the pope of the funds it required to function. Boniface had no option but to swiftly come to terms with Philip. He granted Philip the power to tax the French clergy "during an exigency," and he canonized Louis IX the following year.

Boniface was also besieged at the time by powerful Italian adversaries, whom Philip did not neglect to support. A noble family (the Colonnas), Boniface's adversaries (the Gaetani), and a radical.