Three months after a possessed Gul Dukat killed Jadzia Dax and sealed the wormhole, life on Deep Space Nine has changed. Kira, the acting commander, is upset when Admiral Ross informs her that the Romulans will set up a station office, while Sisko has retreated to Earth to contemplate a way of contacting the Bajoran Prophets — the aliens who reside within the wormhole. When the vision of a woman's face, buried in the sand, appears to Sisko, he sketches her, and Jake Sisko recognizes her from one of his grandfather's photos.
Meanwhile, at the station, Kira meets Cretak, the Romulan Senator, and agrees to let her set up a hospital on an uninhabited Bajoran moon to care for wounded Romulan soldiers. Back on Earth, Sisko asks his father about the woman in the photo, but Joseph, upset, refuses to identify her. Sisko persists and Joseph acquiesces: the woman was his wife, and Sisko's mother.
Joseph explains that the woman, Sarah, left him when Sisko was a baby and later died. Because Sisko's stepmother raised him as her own, Joseph never revealed the truth. He gives Sisko a locket that once belonged to Sarah, and Sisko finds upon it an ancient Bajoran inscription that reads "The Orb of the Emissary." This causes him to wonder if another Bajoran orb exists, which would allow access to the Prophets.
Sisko realizes he must go to the planet Tyree, the setting of his original vision. But while preparing, he is stabbed by a Bajoran who is determined to stop Sisko's quest. Back on Deep Space Nine, Odo shows Kira data indicating that the Romulans are arming the Bajoran moon with plasma torpedoes. Kira demands that Cretak remove the torpedoes — or she will.
Meanwhile, a healed Sisko explains to Jake and Joseph that his attacker was a member of a cult that worships the Pah-wraiths — the enemies of Bajor's Prophets. Joseph realizes that if the attacker knew of Sisko's discovery, the Pah-wraiths must know as well, and Sisko could be in grave danger. He and Jake decide to accompany Sisko to Tyree. But just as the three generations of Siskos are about to leave, a young female Trill arrives at the restaurant. She is Ezri — the new host of the Dax symbiont.