Having thus obtained the indispensable papal confirmation, Constance ruled in Naples as a national queen in the name of the little Frederick. She drove away the German bandits, who had made the name of her husband a terror to her subjects. Markwald of Anweiler left his Apulian fiefs[54] for Romagna. But the Pope joined with Constance in hostility to the Germans. Without Innocent's strong and constant support she could hardly have carried out her policy. Recognizing in the renewal of the old papal protection the best hopes for the independence of Sicily, Constance, on her death in 1198, called on Innocent III to act as the guardian of her son. Innocent loyally took up her work, and struggled with all his might to preserve the kingdom of Frederick against his many enemies. But the contest was a long and a fierce one.

No sooner was Constance dead than the Germans came back to their prey. The fierce Markwald, driven from Romagna by the papal triumph, claimed the regency and the custody of the King. The Saracens and Greeks of Sicily, still numerous and active, joined the Germans. Walter, Bishop of Troja, Chancellor of Sicily, weaved deep plots against his master and his overlord. But the general support of the Church gave Innocent a strong weapon. Roffrid, Abbot of Monte Casino, a tried friend of Henry VI, declared for Innocent against Markwald, who in revenge besieged the great monastery, until a summer storm drove him baffled from its walls. But the purchased support of Pisa gave Markwald the command of the sea, and Innocent had too many schemes on foot and too little military power at his command to be able to make easy headway against him.

At last Innocent had reluctant recourse to Count Walter of Brienne, the French husband of Tancred's daughter Albina, and now a claimant for the hereditary fiefs of Tancred, Lecce, and Taranto, from which, despite Henry VI's promise, he had long been driven. For almost the first time in Italian history, Frenchmen were thus called in to drive out the Germans. But it was then as afterward a dangerous experiment. Walter of Brienne and his small French following invaded Apulia, and fought hard against Diepold of Acerra, another of King Henry's Germans. Meanwhile Markwald, now in open alliance with the Bishop of Troja, made himself master of Sicily and regent of the young King. His death in 1202 removed the most dangerous enemy of both Innocent and Frederick. But the war dragged on for years in Apulia, especially after Diepold had slain Walter of Brienne. The turbulent feudal barons of Apulia and Sicily profited by this long reign of anarchy to establish themselves on a permanent basis. At last Innocent sent his own brother, Richard, Count of Segni, to root out the last of the Germans. So successful was he that, in 1208, the Pope himself visited the kingdom of his ward, and arranged for its future government by native lords, helped by his brother, who now received a rich Apulian fief. It was Innocent's glory that he had secured for Frederick the whole Norman inheritance. It was amid such storms and troubles that the young Frederick grew up to manhood.

In Central and Northern Italy, Innocent III was more speedily successful than in the South. On Philip of Swabia's return to Germany, Tuscany and the domains of the Countess Matilda fell away from their foreign lord, and invoked the protection of the Church. The Tuscan cities formed themselves into a new league under papal protection. Only Pisa, proud of her sea power, wealth, and trade, held aloof from the combination. It seemed as if, after a century of delays, the papacy was going to enjoy the inheritance of Matilda,[55] and Innocent eagerly set himself to work to provide for its administration. In the north the Pope maintained friendly relations with the rival communities of the Lombard plain. But his most immediate and brilliant triumph was in establishing his authority over Rome and the Patrimony of St. Peter. On his accession he found his lands just throwing off the yoke of the German garrisons that had kept them in subjection during Henry VI's lifetime. He saw within the city power divided between the præfectus urbis, the delegate of the Emperor, and the summus senator, the mouthpiece of the Roman commune.

Within a month the prefect ceased to be an Imperial officer, and became the servant of the papacy, bound to it by fealty oaths, and receiving from it his office. Within a year the senator also had become the papal nominee, and the whole municipality was controlled by the Pope. No less complete was Innocent's triumph over the nobility of the Campagna. He drove Conrad of Urslingen back to Germany, and restored Spoleto to papal rule. He chased Markwald from Romagna and the March of Ancona to Apulia, and exercised sovereign rights even in the most remote regions that acknowledged him as lord. If it was no very real sway that Innocent wielded, it at least allowed the town leagues and the rustic nobility to go on in their own way, and made it possible for Italy to work out its own destinies. More powerful and more feared in Italy than any of his predecessors, Innocent could contentedly watch the anti-imperial reaction extending over the Alps and desolating Germany by civil war.

Despite the precautions taken by Henry VI, it was soon clear that the German princes would not accept the hereditary rule of a child of three. Philip of Swabia abandoned his Italian domains and hurried to Germany, anxious to do his best for his nephew. But he soon perceived that Frederick's chances were hopeless, and that it was all that he could do to prevent the undisputed election of a Guelf. He was favored by the absence of the two elder sons of Henry the Lion. Henry of Brunswick the eldest, the Count Palatine of the Rhine, was away on a crusade, and was loyal to the Hohenstaufen, since his happy marriage with Agnes. The next son Otto, born at Argenton during his father's first exile, had never seen much of Germany. Brought up at his uncle Richard of Anjou's court, Otto had received many marks of Richard's favor, and looked up to the chivalrous, adventurous King as an ideal of a warrior prince. Richard had made him Earl of Yorkshire, and had invested him in 1196 with the country of Poitou, that he might learn war and statecraft in the same rude school in which Richard had first acquainted himself with arms and politics. Even now Otto was not more than seventeen years of age. Richard himself, as the new vassal of the Empire for Aries and England, was duly summoned to the electoral diet, but his representatives impolitically urged the claims of Count Henry, who was ruled ineligible on account of his absence. Thus it was that when the German magnates at last met for the election on the 8th of March, 1198, at Muehlhausen, their choice fell on Philip the Arabian, who took the title of Philip II.

Many of the magnates had absented themselves from the diet at Muehlhausen, and an irreconcilable band of partisans refused to be bound by its decisions. Richard of England now worked actively for Otto, his favorite nephew, and found support both in the old allies of the Angevins in the Lower Rhineland and the ancient supporters of the house of Guelf. Germany was thus divided into two parties, who completely ignored each other's acts. Three months after the diet of Muehlhausen, another diet met at Cologne and chose Otto of Brunswick as King of the Romans. Three days afterward the young prince was crowned at Aachen.

A ten-years' civil war between Philip II and Otto IV now devastated the Germany that Barbarossa and Henry VI had left so prosperous. The majority of the princes remained firm to Philip, who also had the support of the strong and homogeneous official class of ministeriales that had been the best helpers of his father and brother. Nevertheless, Otto had enough of a party to carry on the struggle. On his side was Cologne, the great mart of Lower Germany, so important from its close trading relations with England, and now gradually shaking itself free of its archbishops. The friendship of Canute of Denmark and the Guelf tradition combined to give him his earliest and greatest success in the North. It was the interest of the baronage to prolong a struggle which secured their own independence at the expense of the central authority. Both parties looked for outside help. Otto, besides his Danish friends, relied on his uncle Richard, and, after his death, on his uncle John. Philip formed a league with his namesake Philip of France. But distant princes could do but little to determine the result of the contest. It was of more moment that both appealed to Innocent III, and that the Pope willingly accepted the position of arbiter. "The settlement of this matter," he declared, "belongs to the apostolic see, mainly because it was the apostolic see that transferred the Empire from the East to the West, and ultimately because the same see confers the Imperial crown."

In March, 1201, Innocent issued his decision. "We pronounce," he declared, "Philip unworthy of empire, and absolve all who have taken oaths of fealty to him as king. Inasmuch as our dearest son in Christ, Otto, is industrious, discreet, strong, and constant, himself devoted to the Church and descended on each side from a devout stock, we, by the authority of St. Peter, receive him as king, and will in due course bestow upon him the imperial crown." The grateful Otto promised in return to maintain all the possessions and privileges of the Roman Church, including the inheritance of the countess Matilda.

Philip of Swabia still held his own, and the extravagance of the papal claim led to many of the bishops as well as the lay magnates of Germany joining in a declaration that no former pope had ever presumed to interfere in an imperial election. But the swords of his German followers were a stronger argument in favor of Philip's claims than the protests of his supporters against papal assumptions. As time went on, the Hohenstaufen slowly got the better of the Guelfs. With the falling away of the North, Otto's cause became distinctly the losing one. In 1206, Otto was defeated outside the walls of Cologne, and the great trading city was forced to transfer its obedience to his rival. In 1207 Philip became so strong that Innocent was constrained to reconsider his position, and suggested to Otto the propriety of renouncing his claims. But in June, 1208, Philip was treacherously murdered at Bamberg by his faithless vassal, Otto of Wittelsbach, to whom he had refused his daughter's hand. It was no political crime, but a deed of private vengeance. It secured, however, the position of Otto, for the ministeriales now transferred their allegiance to him, and there was no Hohenstaufen candidate ready to oppose him. Otto, moreover, did not scruple to undergo a fresh election which secured for him universal recognition in Germany. By marrying Beatrice, Philip of Swabia's daughter, he sought to unite the rival houses, while he conciliated Innocent by describing himself as King "by the grace of God and the Pope." Next year he crossed the Alps to Italy, and bound himself by oath, not only to allow the papacy the privileges that he had already granted, but to grant complete freedom of ecclesiastical elections, and to support the Pope in his struggle against heresy. In October, 1209, he was crowned Emperor at Rome. After ten years of waiting, Innocent, already master of Italy, had procured for his dependent both the German kingdom and the Roman Empire.