The back-and-forth situation between Empire and papacy repeats again in 1242 and 1243.

Frederick has lobbies unsuccessfully for the election of a lenient pontiff, but the wily cardinal Sinibaldo Fieschi, a believer in the universal authority of the papacy, becomes Pope Innocent IV on June 25, 1243.

He is a member of a noble Imperial family and has some relatives in Frederick's camp, so the Emperor is initially happy with his election.

Innocent, however, is to become his fiercest enemy.

Negotiations had begun in the summer of 1243, but …

...the situation changes as Viterbo rebels, instigated by the intriguing Cardinal Ranieri of Viterbo.

Frederick cannot afford to lose his main stronghold near Rome, and besieges the city.

(Many authorities state that the Emperor's star began its descent with this move.)

Innocent convinces him to withdraw his troops, but Ranieri nonetheless has the Imperial garrison slaughtered on November 13.

Frederick is enraged.

The new Pope is a master diplomat.

Entering Rome in 1244 a triumphant procession, Innocent forces a lopsided peace on Frederick in an attempt to centralize and strengthen papal power.

Frederick begins to issue demands contrary to the peace agreement, eventually causing Innocent to show his true Guelph face.

Together with most of the Cardinals, Innocent flees via Genoese galleys to the Ligurian republic, arriving on July 7.

His aim is to reach Lyon.

Imperial forces attack Piacenza in 1245.

Innocent IV and Frederick II continue the struggle between the Papacy and the Empire.

The pope, forced by the emperor to flee Rome for France in 1244, establishes a papal court-in-exile at the powerful archbishopric of Lyon.

Innocent condemns the emperor in April 1245, and summons him to appear before the Council of Lyon, which convenes successfully despite Frederick’s blocking of the Alpine passes to France; he has captured and imprisoned clerics on their way to the Council.

When Frederick refuses to appear, Innocent induces the council to convict him in absentia and declare him deposed on a triple charge: constant violation of the peace, sacrilege, and heresy.

The pope then attempts to secure the election of a new emperor.

, and in April 1245, he was formally deposed by Innocent IV.

Pope Gregory IX had also earlier offered King Louis' brother, count Robert of Artois, the German throne, but Louis had refused.

The ecumenical council also attempts to assist the Christian forces fighting in the Holy Land and to organize a defense against the Mongol invasion of Europe.

The capture of Jerusalem by the Khwarezmians, recently displaced by the advance of the Mongols, on their way to ally with Egypt, has returned Jerusalem to Muslim control, but European Christians have seen the city pass from Christian to Muslim control numerous times in the past two centuries.

This time, despite calls from the Pope, there is no popular enthusiasm for a new crusade.

The only man interested in beginning one is Louis IX, who declares his intent to go East in 1245.

The Holy Roman Emperor is in no position to crusade.

Béla IV of Hungary is rebooting his devastated kingdom after the Mongol invasion of 1241.

Henry III of England is still struggling with Simon de Montfort, among other his other problems.

Henry and Louis, engaged as they are in the Capetian-Plantagenet struggle, are not on good terms.

A new papal council had been held in Lyon beginning on June 24, 1245.

One month later, Innocent IV had declared Frederick to be deposed as emperor, characterizing him as a "friend of Babylon's sultan", "of Saracen customs", "provided with a harem guarded by eunuchs" like the schismatic emperor of Constantinople, and, in sum, a "heretic".

The Pope backs Henry Raspe, landgrave of Thuringia as his rival for the imperial crown and sets in motion a plot to kill Frederick and Enzio, supported by another friend of Frederick's, Orlando de Rossi, the pope's brother-in-law.

The count of Caserta unmasked the plotters, and the vengeance is terrible: the city of Altavilla Silentina, where they had found shelter, and which had sided with the town of Capaccio and other local barons against the emperor Frederick II, is razed to the ground, and the guilty are blinded, mutilated and burned alive or hanged.

An attempt to invade the Kingdom of Sicily, under the command of Ranieri, is halted at Spello by Marino of Eboli, Imperial vicar of Spoleto.

Papal-influenced rebellion in Sicily develops against the Holy Roman empire in 1245-46.

Innocent IV also sends a flow of money to Germany to cut off Frederick's power at its source.

The archbishops of Cologne and Mainz have also declared Frederick deposed, and in May 1246 a new king had been chosen in the person of Henry Raspe.

Henry, thanks to the Pope's money, manages on August 5, 1246, to defeat an army of Conrad, son of Frederick, near Frankfurt.

Frederick has strengthened his position in Southern Germany, acquiring the Duchy of Austria, whose duke had died without heirs, and one year later, Henry Raspe dies as well.

The new anti-king is William II, Count of Holland, the son of Floris IV and Matilda of Brabant.

William was only seven years old when his father was killed at a tournament at Corbie, His uncles William and Otto (Bishop of Utrecht) had been his guardians until 1239.

With the help of Henry II, Duke of Brabant and the archbishop of Cologne, William is elected in 1247 as king of Germany after Emperor Frederick II is excommunicated.