The coronation of Otto IV did not end Innocent's troubles with the Empire. It was soon followed by an open breach between the Pope and his nominee, from which ultimately developed something like a general European war, between a league of partisans of the Pope and a league of partisans of Otto. It was inevitable that Otto, as a crowned emperor, should look upon the papal power in a way very different from that in which he had regarded it when a faction leader struggling for the crown. Then the support of the Pope was indispensable. Now the autocracy of the Pope was to be feared. The Hohenstaufen ministeriales, who now surrounded the Guelfic Emperor, raised his ideals and modified his policy. Henry of Kalden, the old minister of Henry VI, was now his closest confidant, and under his direction it soon became Otto's ambition to continue the policy of the Hohenstaufen. The great object of Henry VI had been the union of Sicily with the Empire. To the alarm and disgust of Innocent, his ancient dependent now strove to continue Henry VI's policy by driving out Henry VI's son from his Sicilian inheritance. Otto now established relations with Diepold and the other German adventurers, who still defied Frederick II and the Pope in Apulia. He soon claimed the inheritance of Matilda as well as the Sicilian monarchy. In August, 1210, he occupied Matilda's Tuscan lands, and in November invaded Apulia, and prepared to despatch a Pisan fleet against Sicily. Innocent was moved to a terrible wrath. On hearing of the capture of Capua, and the revolt of Salerno and Naples, he excommunicated the Emperor and freed his subjects from their oaths of fealty to him. But, despite the threats of the Church, Otto conquered most of Apulia and was equally successful in reviving the Imperial authority in Northern Italy.
Innocent saw the power that he had built up so carefully in Italy crumbling rapidly away. In his despair he turned to France and Germany for help against the audacious Guelf. Philip Augustus, though still in bad odor at Rome through his persistent hostility to Ingeborg, was now an indispensable ally. He actively threw himself into the Pope's policy, and French and papal agents combined to stir up disaffection against Otto in Germany. The haughty manners and the love of the young King for Englishmen and Saxons had already excited disaffection. It was believed that Otto wished to set up a centralized despotism of court officials, levying huge taxes on the model of the Angevin administrative system of his grandfathers and uncles. The bishops now took the lead in organizing a general defection from the absent Emperor. In September, 1211, a gathering of disaffected magnates, among whom were the newly made king Ottocar of Bohemia and the dukes of Austria and Bavaria, assembled at Nuremberg. They treated the papal sentence as the deposition of Otto, and pledged themselves to elect as their new king Frederick of Sicily, the sometime ward of the Pope. It was not altogether good news to the Pope that the German nobles had, in choosing the son of Henry VI, renewed the union of German and Sicily. But Innocent felt that the need of setting up an effective opposition to Otto was so pressing that he put out of sight the general in favor of the immediate interests of the Roman see. He accepted Frederick as emperor, only stipulating that he should renew his homage for the Sicilian crown, and consequently renounce an inalienable union between Sicily and the Empire. Frederick now left Sicily, repeated his submission to Innocent at Rome, and crossed the Alps for Germany.
Otto had already abandoned Italy to meet the threatened danger in the North. Misfortunes soon showered thick upon him. His Hohenstaufen wife, Beatrice, died, and her loss lessened his hold on Southern Germany. When Frederick appeared, Swabia and Bavaria were already eager to welcome the heir of the mighty southern line, and aid him against the audacious Saxon. The spiritual magnates flocked to the side of the friend and pupil of the Pope. In December, 1212, followed Frederick's formal election and his coronation at Mainz by the archbishop Siegfried. Early in 1213 Henry of Kalden appeared at his court. Henceforward the important class of the ministeriales was divided. While some remained true to Otto, others gradually went back to the personal representative of Hohenstaufen.
Otto was now thrown back on Saxony and the Lower Rhineland. He again took up his quarters with the faithful citizens of Cologne, when he appealed for help to his uncle, John of England, still under the papal ban. With English help he united the princes of the Netherlands in a party of opposition to the Pope and the Hohenstaufen. Frederick answered by a closer and a more effective league with France. Even before his coronation he had met Louis, the son of Philip Augustus, at Vaucouleurs. All Europe seemed arming at the bidding of the Pope and Emperor.
John of England now hastily reconciled himself to Innocent, at the price of the independence of his kingdom. He thus became in a better position to aid his excommunicated nephew, and revenge the loss of Normandy and Anjou on Philip Augustus. His plan was now a twofold one. He himself summoned the barons of England to follow him in an attempt to recover his ancient lands on the Loire. Meanwhile, Otto and the Netherlandish lords were encouraged, by substantial English help, to carry out a combined attack on France from the north. The opposition of the English barons reduced to comparative insignificance the expedition to Poitou, but a very considerable army gathered together under Otto, and took up its position in the neighborhood of Tournai. Among the French King's vassals, Ferrand, Count of Flanders, long hostile to his overlord Philip, and the Count of Boulogne fought strenuously on Otto's side; while, of the Imperial vassals, the Count of Holland and Duke of Brabant (Lower Lorraine) were among Otto's most active supporters. A considerable English contingent came also, headed by Otto's bastard uncle, William Longsword, Earl of Salisbury. Philip himself commanded the chivalry of France, leaving his son Louis to fight against John in Poitou. On July 27th the decisive battle was fought at Bouvines, a few miles southwest of Tournai. The army of France and Church gained an overwhelming victory over the league which had incurred the papal ban, and Otto's fortunes were utterly shattered. He soon lost all his hold over the Rhineland, and was forced to retreat to the ancient domains of his house in Saxony. His remaining friends made their peace with Philip and Frederick. The defection of the Wittelsbachers lost his last hold in the south of Germany, and the desertion of Valdemar of Denmark deprived him of a strong friend in the North. John withdrew from Continental politics to be beaten more decisively by his barons than he had been beaten in Poitou or at Bouvines.
Frederick II, was now undisputed King of the Romans, and Innocent III had won another triumph. By the Golden Bull of Eger (July, 1213) Frederick had already renewed the concessions made by Otto to the Church, and promised obedience to the holy see. In 1216 he pledged himself to separate Sicily from the Empire, and establish his son Henry there as king, under the supremacy of the Church. But, like his other triumphs, Innocent's victory over the Empire was purchased at no small cost. For the first time, a German national irritation at the aggressions of the papacy began to be distinctly felt. It found an adequate expression in the indignant verses of Walther von der Vogelweide, protesting against the priests who strove to upset the rights of the laity, and denouncing the greed and pride of the foreigners who profited by the humiliation of Germany.
Amid all the distractions of western politics, Innocent III ardently strove to revive the crusading spirit. He never succeeded in raising all Europe, as several of his predecessors had done. But after great efforts, and the eloquent preaching of Fulk of Neuilly he stirred up a fair amount of enthusiasm for the crusading cause, and, in 1204, a considerable crusading army, mainly French, mustered at Venice. It was the bitterest disappointment of Innocent's life that the Fourth Crusade never reached Palestine, but was diverted to the conquest of the Greek empire. Yet the establishment of a Catholic Latin empire at Constantinople, at the expense of the Greek schismatics, was no small triumph. Not disheartened by his first failure, Innocent still urged upon Europe the need of the holy war. If no expedition against the Saracens of Syria marked the result of his efforts, his pontificate saw the extension of the crusading movement to other lands. Innocent preached the crusade against the Moors of Spain, and rejoiced in the news of the momentous victory of the Christians at Navas de Tolosa. He saw the beginnings of a fresh crusade against the obstinate heathen on the eastern shores of the Baltic.
But all these crusades were against pagans and infidels. Innocent made a much greater new departure when he proclaimed the first crusade directed against a Christian land. The Albigensian crusade succeeded in destroying the most dangerous and widespread popular heresy that Christianity had witnessed since the fall of the Roman Empire, and Innocent rejoiced that his times saw the Church purged of its worst blemish. But in extending the benefits of a crusade to Christians fighting against Christians, he handed on a precedent which was soon fatally abused by his successors. In crushing out the young national life of Southern France the papacy again set a people against itself. The denunciations of the German Minnesinger were reechoed in the complaints of the last of the Troubadours. Rome had ceased to do harm to Turks and Saracens, but had stirred up Christians to war against fellow-Christians. God and his saints abandon the greedy, the strife-loving, the unjust worldly Church. The picture is darkly colored by a partisan, but in every triumph of Innocent there lay the shadow of future trouble.
Crusades, even against heretics and infidels, are the work of earthly force rather than of spiritual influence. It was to build up the great outward corporation of the Church that all these labors of Innocent mainly tended. Even his additions to the canon law, his reforms of ecclesiastical jurisdiction, dealt with the external rather than the internal life of the Church. The criticism of James of Vitry, that the Roman curia was so busy in secular affairs that it hardly turned a thought to spiritual things, is clearly applicable to much of Innocent's activity. But the many-sided Pope did not ignore the religious wants of the Church. His crusade against heresy was no mere war against enemies of the wealth and power of the Church. The new tendencies that were to transform the spiritual life of the thirteenth century were not strange to him. He favored the early work of Dominic; he had personal dealings with Francis, and showed his sympathy with the early work of the poor man of Assisi. But it is as the conqueror and organizer rather than the priest or prophet that Innocent made his mark in the Church. It is significant that, with all his greatness, he never attained the honors of sanctity.
Toward the end of his life, Innocent held a general council in the basilica of St. John Lateran. A vast gathering of bishops heads of orders, and secular dignitaries gave brilliancy to the gathering and enhanced the glory of the Pontiff. Enthroned over more than four hundred bishops, the Pope proudly declared the law to the world. "Two things we have specially to heart," wrote Innocent, in summoning the assembly, "the deliverance of the Holy Land and the reform of the Church Universal." In its vast collection of seventy canons, the Lateran Council strove hard to carry out the Pope's programme. It condemned the dying heresies of the Albigenses and the Cathari, and prescribed the methods and punishments of the unrepentant heretic. It strove to rekindle zeal for the crusade. It drew up a drastic scheme for reforming the internal life and discipline of the Church. It strove to elevate the morals and the learning of the clergy, to check their worldliness and covetousness, and to restrain them from abusing the authority of the Church through excess of zeal or more corrupt motives. It invited bishops to set up free schools to teach poor scholars grammar and theology. It forbade trial by battle and trial by ordeal. It subjected the existing monastic orders to stricter superintendence, and forbade the establishment of new monastic rules. It forbade superstitious practices and the worship of spurious or unauthorized relics.