It’s explicitly stated by the Netherbrain in act 3 that they allowed the Emperor to escape their thrall, anticipating all of the events leading to him discovering Orpheus and your adventuring party - as well as the the chosen of the Dead 3 discovering the Crown of Karsus and the Ilithid oubliette under Moonrise Towers. It is implied that the whole idea for the creation of the Cult of the Absolute and planned power grab by the Dead 3 was also anticipated/orchestrated by the brain from the beginning.