An old Bajoran light ship comes through the Wormhole, and its passenger, Akorem, claims that he is the Emissary of the Prophets. Akorem is well known in Bajoran history as a poet, with many widely read masterworks such as Kitara's Song, Gaudaal's Lament and The Call of the Prophets. Jadzia Dax estimates the ship to be 300 years old, however, Akorem states a date as being only 200 years in the past.
At first, Sisko is happy to give up his position as a religious leader for the Bajorans. Soon, disturbing things come to light. Akorem wishes to return Bajor to a system of "dejara" caste-based discrimination. This would also result in the Federation denying Bajor for membership, as such discrimination is forbidden under Federation law.
Sisko must deal with a vision of Kai Opaka, as well as the murder of a 'lower caste' Bajoran (executed by a Vedek for not following his caste) and his second in command, Kira deciding she should resign her post to follow her caste.
Sisko challenges Akorem and they both enter the wormhole to see what the Prophets think. It turns out Akorem was a challenge for Sisko, forcing him to accept his role. Akorem is sent back to his own time, to live out his life with no memory of his two hundred year long trip. Akorem's return to the past causes history to change, but people's memories of it remain unchanged. For example, Kira Nerys remembers that Akorem's work on The Call of the Prophets was unfinished when he disappeared. Reading it again however, she finds that additional stanzas now exist.