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.

Despite his preoccupation with Italy and Germany, the early years of Innocent’s pontificate saw him busily engaged in upholding the papal authority and the moral order of the Church in every country in Europe.  No consideration of the immediate interests of the Roman see ever prevented him from maintaining his principles even against powerful sovereigns who could do much to help forward his general plans.  The most conspicuous instance of this was Innocent’s famous quarrel with Philip Augustus of France, when to vindicate a simple principle of Christian morals he did not hesitate to abandon the alliance of the “eldest son of the Church” at a time when the fortunes of the papacy were everywhere doubtful.  Philip’s first wife, Isabella of Hainault, the mother of the future Louis VIII, had died in 1190, just before her husband had started on his crusade.  In 1193 Philip negotiated a second marriage with Ingeborg, the sister of Canute VI, the powerful King of Denmark, hoping to obtain from his Danish brother-in-law substantial