Despite the fact that he was illegitimate, Calaxes wasn't in the line of succession to the Imperial throne, he had been given Archbishopric of The One: a powerful position in the Imperial City, and indeed over all Tamriel where that religion is honored.
Rumors began to spread that Calaxes believed that the Gods were angered by the state of current Empire and the Emperor himself. It was even said that Calaxes advocated full-scale rebellion to establish a theocracy over the Empire. And it was certainly true that the relationship between Calaxes and the Emperor had become very stormy.
One day Calaxes simply disappeared without leaving any trace. Some believe he was removed by the Imperial Guard as they saw him as a threat to the Emperor. It is suggested that the Lady Allena Benoch had something to do with his disappearance.
- The date of Calaxes' disappearance is recorded to be Sun's Dusk of 3E 498. However, that is impossible due to the fact that the date simply does not exist. 3E 433 is the last year of Third Era. Words and Philosophy, the book where he is mentioned, also appears in The Elder Scrolls III: Morrowind, which takes place in 3E 427.