Benedict IX's forces return in April 1045 and expel his rival, who returns to his previous bishopric.

Later in 1045, in order to rid the Church of the scandalous Benedict, his godfather, the pious priest John Gratian, persuades Benedict to resign the papacy for a sum of money, thus allowing Gratian to become Pope Gregory VI.

Some also say that Benedict wanted to marry.

Benedict IX soon regrets his resignation and returns to Rome, taking the city; he will remain on the throne until July 1046, although Gregory VI continues to be recognized as the true pope.

At this time, Sylvester III also reasserts his claim.