An old Bajoran light ship comes through the Wormhole, and its passenger, Akorem Laan (Richard Libertini), claims to be 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. Lt. Cmdr. Dax (Terry Farrell) estimates the ship to be 300 years old, however, Akorem states a date as being only 200 years in the past.
At first, Captain Sisko (Avery Brooks) is happy to give up his position as a religious leader for the Bajorans (which Starfleet has never approved of). However, disturbing things soon come to light. Akorem believes that Bajor has lost its way as a result of abandoning the "d'jarra", a caste-based system, in order to resist the CardassianOccupation, and it must return to that old practice. This would result in the Federation denying membership for Bajor (which Starfleet considers to be a failure of Sisko's mission), as caste-based discrimination is forbidden under Federation law. Sisko must deal with losing his First Officer as Major Kira (Nana Visitor) must now live in the "d'jarra" of an artist, a vision of Kai Opaka (Camille Saviola) questioning his (Sisko's) self-identity and the murder of a 'lower caste' Bajoran (executed by Vedek Porta (Robert Symonds) for not following his caste).
Sisko challenges Akorem to regain the office of Emissary, and the two agree to enter the wormhole and ask the Prophets who it should be. 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, Major Kira 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.
In a subplot, Chief Miles O'Brien (Colm Meaney) tries to deal with the news of his wife Keiko (Rosalind Chao) being pregnant again. Though everyone gives their congratulations, Miles seems at odds about having a second child, thinking about how it will change his ability to spend time with Keiko, though even in the present Keiko seems too busy with work. Keiko's return also disrupts Miles' and Dr. Bashir's (Alexander Siddig) usual time together, which Keiko senses and contrives to remedy.