As Chief O'Brien and Doctor Bashir enter the O'Briens' quarters, having just won the Battle of Britain in the holosuite, they lament that O'Brien must return the quarters to normal in preparation for Keiko's return. O'Brien greets Keiko and Molly warmly at the airlock and receives a surprise: During Keiko's last visit to Deep Space 9, they got lucky in their attempt to conceive a child, which means he will not be getting lucky tonight.
While O'Brien welcomes his family back to the station, Major Kira welcomes Vedek Porta to Ops. The Vedek has brought a Bajoran couple, who wish for Captain Sisko, as the Emissary of the Prophets, to bless their upcoming marriage. After he agrees and they leave, he remarks to Dax how much he wishes he wasn't the Emissary. Then something comes through the Bajoran wormhole – a Bajoran lightship, which appears to be 200 years old. The passenger, a lone man, is beamed to the infirmary. When Sisko and Kira get there, the man introduces himself; he is the Emissary.
The mysterious man is Akorem Laan, a famous Bajoran poet from the 22nd century whose unfinished poem, The Call of the Prophets, has become legendary. He explains that, while traveling in his lightship, he was injured and thought he would die. Then he discovered the wormhole by mistake and was healed by the Prophets, who have delivered him to DS9. He knows nothing of the Cardassian occupation or other hardships his people have been through, but he believes the Prophets have chosen him as their Emissary.
As Sisko tries to convince himself that he is glad to give up his role as Emissary, Akorem learns that during the occupation, the Bajoran people gave up their d'jarras, a stratified caste system based on family names. He announces to the Bajorans on DS9 that the Prophets have sent him to bring back the d'jarras and help the Bajoran people find their way again. Sisko informs Akorem that if Bajor adopts a caste-based discrimination system, then they will be ineligible for entry into the Federation. Akorem sees it as an acceptable sacrifice, as does – not surprisingly – Kai Winn. Even Kira will go along with the plan, as it is not her place to question the Emissary. In the Replimat, Sisko is having a drink agonizing over recent events when Kira approaches. She is unable to find a seat in the Replimat and is about to leave when a Bajoran woman gives her seat to Kira, simply because she has a higher d'jarra – something which Sisko informs Kira has been happening all over the station. The two are troubled by the immediate change on the station.
Unable to sleep, Sisko wanders about the Promenade that night, where he has visions of Kai Opaka. She asks who he is and claims he does not know himself. When Sisko asks Bashir about the vision, he describes it as an orb shadow, which the Bajorans believe occur when a person is not following the will of the Prophets as shown in the orbs. Religious explanations aside, it was caused by an over-abundance of neuropeptides, and Sisko readily accepts treatment to make the visions stop.
Kira attempts to follow her d'jarra, which dictates that she is to be an artist. Unfortunately, despite her best attempts, she ends up with a "flock of flightless birds" in her quarters. Vedek Porta is nonetheless stern in his belief that d'jarras are correct and that the Prophets have chosen for Kira to be an artist.
Meanwhile, O'Brien and Bashir meet by chance in Quark's and realize they no longer have time for one another now that Keiko and Molly are back on the station. O'Brien attempts to play darts with Molly in their quarters, and Bashir tries to teach Morn how to play in the bar, but it is not the same for either of them.
Meanwhile things are going from bad to worse for Sisko. His failure in his mission to ensure Bajor's entry into the Federation, a goal Sisko has been working toward for several years now, does not please Starfleet Command. Although there is no direct statement of it, he can tell they are unhappy, which he finds ironic considering they never wanted him to be the Emissary in the first place. As he and Kira go over the duty roster, he cannot shake the feeling that he has failed in his duties. And it gets worse: Kira has to resign in order to follow her d'jarra. As soon as Sisko can find someone to take her post, she'll leave. There is an extremely sad moment between them as reality sets in.
While O'Brien and Bashir try to deal with their withdrawal, Sisko gets a call from Odo to come to the Promenade immediately, where a vedek has just been killed. The man, Vedek Imutta, fell from the second level, and as Odo prepares to start an investigation, Vedek Porta calmly announces that he pushed the man simply because he had an "unclean" d'jarra and was unwilling to resign as Vedek to follow his d'jarra. Sisko decides that enough is enough and he must take back his role as emissary from Akorem. However, as Akorem is unwilling to give up the post and both men know there will be chaos if they force the Bajoran people to choose between them, they enter the wormhole to ask the Prophets to choose.
Inside the wormhole, Akorem remains convinced that he is the emissary, but as usual, the Prophets appear largely unconcerned. They claim Sisko and Akorem's linear nature limits their comprehension. They do say that the d'jarras are in the past, which Sisko has taught them means it is no more and it can never be again. The Prophets explain that they sent Akorem into the future "for the Sisko." After weighing the options, Akorem has them send him back to his own time. They tell Sisko he is "of Bajor," as the Prophets are "of Bajor," before returning him as well.
Back on the station, Keiko has devised a plan to help her husband. She sets him up and calls Bashir, informing him of Miles' recent depression, and asks the doctor to help him with it. The two of them get their dart game after all. Meanwhile Sisko is reading The Call of the Prophets, which Kira is surprised to learn is now finished. As the two consider why they can still remember the altered timeline, a Bajoran man and his daughter approach the officers to ask Sisko if he can bless the girl at her upcoming birthday celebration. Sisko happily agrees to the request, having now fully accepted his role as the Emissary.