It's been three months since Captain Sisko left DS9. The recently-promoted Colonel Kira is in charge of the station, but since the wormhole closed, all is not well. The crew is concerned that the captain may not come back, and Worf is frustrated with convoy duty. The Romulans set up a post on the station, which seems to work out at first, but things get tense when they establish a hospital facility in the Bajoran system only to fortify it with heavy weapons.In New Orleans, Ben has hardly left his father's restaurant since they got there. Joseph and Jake are increasingly concerned, but when Ben's baseball rolls off the piano he's playing, Ben has a vision - on the desert planet Tyree, he uncovers the face of a woman.Ben is stunned to find out that his father has a picture of that woman - a picture Jake happened to find while cleaning one day. Joseph is reluctant to discuss it at first, but finally reveals that the woman - Sarah - is Ben's real mother, that she had left around the time Ben had his first birthday, and that she died before Joseph could find her again. Things become weirder when Joseph gives Ben a necklace that belonged to Sarah, on which ancient Bajoran text is inscribed. The text refers to "the Orb of the Emissary", which had never been referenced before in Bajoran history. While contemplating what this means, Ben is attacked by a member of the Cult of the Pah-Wraiths; this doesn't dissuade him, however, as he has concluded that the Orb must be on Tyree, and he is determined to search for it.Chief O'Brien learns that Worf's frustrations are due to his belief that Jadzia has not entered Sto'Vo'Kor, the Klingon equivalent of heaven, and that convoy duty has precluded any opportunity to win a battle in her honor, getting her in. O'Brien and Bashir get Martok to enlist Worf's aid on a daring plan to destroy a Cardassian shipyard, and the two Starfleet officers also agree to come along - Bashir because he wants to honor Jadzia as well, and O'Brien to watch out for Bashir. Quark decides that they're all crazy.As he prepares to leave, with Joseph and Jake insisting on going with him, they get a surprise visitor... a young, short Starfleet ensign, a Trill female... who introduces herself as Dax.
- Action Series, Quiet Drama Episode: Previous season openers on DS9 had been as exciting as possible to get the ball rolling on the action. This one was a deliberate inversion of that, with a quiet examination of the effects of the war and Jadzia's death on the main characters.
- Almighty Janitor: The Emissary of the Prophets (who is later revealed to be a borderline demigod) spends a fair amount of time scrubbing clams and playing the piano at his father's restaurant.
- Bitch in Sheep's Clothing: Senator Cretak initially comes off like the nicest Romulan ever, but eventually reveals herself to be duplicitous.
- Call-Back: When O'Brien shares a drink with Worf, he brings up the old days on the Enterprise-D, and Reginald Barclay in particular. This is also notable as being the only time in either series that O'Brien calls Geordi LaForge by his first name.
- Calling the Old Man Out: Sisko chews his father out for not telling him about Sarah.
- Chronic Backstabbing Disorder: Lampshaded by Weyoun re the Romulans.
- Colonel Badass: Kira's been promoted between seasons.
- Don't Call Me "Sir": Kira discourages Odo from calling her by her new rank.
- Hangover Sensitivity: O'Brien learns that trying to keep up with a drinking Klingon results in a bad hangover.
- In Vino Veritas: O'Brien invokes this on Worf to find out why he's been in a bad mood lately. Learns the aforementioned hangover lesson.
- Just Between You and Me: After stabbing Sisko, the Bajoran says "You'll never find the Orb of the Emissary!" He is immediately knocked out by Jake, who then calls for help.
- The Nth Doctor: The episode introduces Ezri Dax.
- One-Liner, Name... One-Liner:Nog: I only wish Captain Sisko were here.
O'Brien: So do I, Ensign. So do I.
- Religion of Evil: While the Pah-Wraiths have been known to the show for some time, we finally meet their worshippers: the Cult of the Pah-Wraiths.
- Smug Snake: Weyoun and Damar definitely enjoy hearing news about the rising tensions between the Romulans and the Bajorans.
- Wham Line: The very last lines of the episode, as Sisko is introduced to Ezri Dax.Ezri: Hello, Benjamin.Sisko: Do I know you?Ezri: It's me. Dax.