On 28 September 1197, Emperor Henry VI, who was just 32 years old, died unexpectedly creating unrest in the circles of the princes about the future direction of the Holy Roman Empire.
There were now opposing forces to the hitherto stable position of the Hohenstaufens, as had already been demonstrated by the failure of Henry VI's Erbreichsplan or "plan for hereditary succession".
Although Frederick had already been elected at the end of 1196 in Frankfurt under the heavy influence of the Archbishop of Mainz, Konrad von Wittelsbach, and Duke of Swabia, Philip, the temptation to switch support away from the former ruling house grew.
The most promising candidate at first was the Duke of Saxony, Bernard III from the House of Ascania, who was able to secure support inter alia from the Archbishop of Cologne, Adolf of Altena.
However, the English king, Richard I proposed his nephew, the then Count of Poitou, Otto of Brunswick, who was the son of the Saxon duke, Henry the Lion.
Under pressure from the Saxon princes, Philip of Swabia who, as the uncle of the young Frederick, had only intended to secure the kingdom for his nephew, finally agreed to his own election as king.
Philip obviously did not share the view of his sister-in-law about the feudal dependence of Sicily on the Pope, and was therefore unwilling to regard the kingdom as a papal fief.
On 20 May 1199, he declared to the Archbishop of Cologne and the other signatories of Otto's letter of recommendation that he would support the Welf king, if the latter showed himself to be loyal to the church.
The political interests of the papacy were crucial to this decision, for Otto had now to back his earlier assurances with documentary evidence, not least the continuing excommunication of Philip.
The pope now intervened energetically in the dispute, banned Philip and his followers including the signatories of the Speyer Declaration, and proceeded with all severity against them.
The Hohenstaufen party reacted with a violent protest at several Hoftage and rejected the interference of the pope in the German election as an unheard-of process.
Through disagreements and losses of power in the east, his own brother, Count Palatine Henry, deserted him, as did even Adolf of Cologne, the creator of his kingdom.
When the Welf emperor was about to attack Sicily in the middle of November, with the aim of restoring the situation to that of 1197, Pope Innocent imposed the imperial ban on Otto and released his subjects from their oaths of loyalty.
This meant Pope Innocent now had to accept another member of a dynasty which he had hitherto demonized as a family of persecutors of the Church, and feared Sicily joining the Empire.
Frederick's one-year-old son, Henry, was crowned King of Sicily at the request of the Pope, and Innocent thus received a kind of insurance.
The first successful outcome of the papal counteraction was that Otto left Sicily in October 1211 and returned to Germany, because his position in the Empire had become fragile.
Once more, as Walther von der Vogelweide sang "the Pope had placed two Germans under one crown, bringing disunity and devastation across the Empire."
On 12 July 1213, he had granted a great privilege to the Church: the Golden Bull of Eger, in which he once again recorded in writing the concessions he had already made to the Curia.
It included recognition of the freedom of episcopal elections, the lands recovered by the Papacy, the Pope's sovereignty over Sicily, and the assurance of aid against heretics.