A centuries old Bajoran vessel mysteriously exits the wormhole, and its passenger, a legendary Bajoran named Akorem Laan, is immediately beamed to the Infirmary. Shocked to learn that more than 200 years have passed since he left Bajor, he tells Sisko and Kira that he had an accident in space and was saved by the Bajoran Prophets, which led him to believe that they have chosen him to be the Emissary. Sisko, who was never comfortable with the assumption that he was Emissary, steps aside to let Akorem assume the revered position. Soon afterward, Akorem makes his first public address, telling the crowd that the prophets chose him to return Bajor to the old ways — including strict adherence to a caste system that restricts people to specific "D'jarras," or occupations.

Sisko is disturbed, since caste-based discrimination goes against the Federation Charter, which will cause Bajor to be excluded from the membership, but Akorem is convinced he is following the wishes of the Prophets. That evening, Sisko is so troubled, he has a nightmare and is unable to get back to sleep. He goes for a walk on the Promenade and encounters a vision of Kai Opaka, who warns Sisko that he does not know himself.

Bashir tells Sisko that he experienced an "Orb Shadow" — a phenomenon encountered by people who've been exposed to the Bajoran orbs, but which only occurs if the advice the Prophets tried to give has been ignored. Later, Sisko reveals to Kira that he believes he has failed in his mission to bring Bajor into the Federation. Kira assures him that it isn't his fault, but complicates his dilemma by telling him she plans to resign her post to follow her D'jarra and become an artist.

Sisko's contemplative mood is interrupted when Odo summons him to the Promenade — a Bajoran monk has died. Vedek Porta states that he is responsible, saying he pushed the man to his death because he refused to resign, even though his family's D'jarra is "unclean." Appalled, Sisko requests another meeting with Akorem and admits that giving up his position as Emissary was a mistake, then reveals that he is forced to challenge Akorem's claim. Since they have no other way of proving which is the real Emissary, Sisko suggests that the two of them go to the wormhole and ask the Prophets.

In the wormhole, the aliens within reveal that Akorem was sent into the future for Sisko — the true Emissary. At Sisko's suggestion, the aliens return the dejected Akorem to his own time, to live out his life without any memory of the future. Sisko is finally convinced that he is the Emissary and ready to handle the responsibility.