In Sisko’s office, Jadzia Dax and Miles O’Brien tell the commander about finding the personnel files kept by Dukat, the previous prefect of Deep Space 9. O’Brien tells Sisko he should probably warn Kira about her file before she can see it. She walks in at that exact moment, and asks what should she be warned about; Sisko tells her she might find the file disappointing, and she assures him she can handle it, and begins to review the file. Moments later, Kira storms out of the room, angry and insulted at how little emphasis she got as a member of the Bajoran resistance.
In the meantime, Julian Bashir tells Sisko that Kai Opaka, who has never left Bajor before, is aboard for an unannounced visit and wishes to have the tour of the station that Sisko previously offered her.
As they show her around the station, Opaka seems unusually distracted. Sisko then notices Opaka standing by the viewport where the wormhole can be best seen. It’s obvious she would like to see the it, but she doesn’t say it. Since there’s nothing scheduled to go through that day, Sisko decides to take her himself on a runabout, accompanied by Kira, and he also allows Bashir to tag along.
Sisko asks O’Brien to prepare the USS Yangtzee Kiang, and as the group is boarding, Opaka pauses to give O’Brien a necklace she was wearing, and asks him to give it to his daughter. He sees them off, a bit puzzled.
Sisko takes the Yangtzee Kiang through the wormhole, and Opaka is amazed and emotionally moved by the spectacle of the interior. Sisko remarks that she’ll see in a few years just what it is worth to Bajor, and is ready to head back. Opaka, who is seemingly waiting for something, is disappointed, until they pick up a narrow band subspace signal and insists they investigate it before leaving the Gamma Quadrant.
They identify the source as a planet orbited by artificial satellites, one of which seems to be malfunctioning. Bashir identifies a habitable moon with possible lifeforms, when suddenly one of the satellites comes near the runabout and fires. The runabout is badly damaged and starts to descend towards the moon, and while the officers fight for control, Opaka is not fearful but strangely content as the ship crash lands.
On the planet’s surface, Sisko, Bashir, and Kira, leave the runabout, carrying out the unconscious Kai. Unfortunately, Bashir soon pronounces her dead, and Kira mourns. As they stand by the runabout, they realize they are not alone, and are quickly surrounded by a group of armed people.
Meanwhile, on DS9, the Yangtzee Kiang is now three and a half hours overdue. O’Brien and Dax prepare the USS Rio Grande to find the missing crew. Odo must handle the frequent messages from Bajor on the Kai’s status, as they were informed she went into the wormhole. He can only tell them they have a lead on where they are at the moment. Dax asks Odo to have the Bajorans have a vessel on the Gamma Quadrant side of the wormhole to relay messages via subspace.
On the planet, the crew is taken by the Ennis, a humanoid species, and they escort them into the caves with weapons in hand. They are obviously cautious of them. The apparent leader, Golin Shel-la, is suspicious, but Sisko is able to convince him they are not hostile. Shel-la permits Bashir to help Kira with her wounds. He explains that they live along with their enemies the Nol-Ennis on the moon, which serves as a penal colony, to which both groups were banished after their homeworld’s mediators were unable to negotiate peace between the two factions. Now that the Starfleet crew is with them, they will be considered their allies and in danger, even though a rescue team is probably on the way.
The Nol-Ennis suddenly attack the area and the prisoners immediately start the firefight. Several soldiers are killed from each faction before Kira puts an end to the skirmish by bringing down part of the cave ceiling with a Starfleet phaser, despite Sisko’s desire not to get involved. Just then, the silhouette of the Kai unexpectedly appears in the cave entrance. She is alive.
Bashir examines the Kai, who appears normal and healthy. She says she only remembers the crash, but then nothing. She gets up and walks to see the area. Bashir further says her physiology is radically different, with an inexplicable biomechanical presence in her cells. He needs to do a full analysis to see what’s going on. Interestingly, the other fallen soldiers similarly begin to revive.
Meanwhile, O’Brien and Dax are able to trace the Yangtzee Kiang‘s [warp eddy] current to the system, and head there.
O’Brien is confused that they aren’t even picking up the ship’s transponder signal, which will make the search difficult. Adding to the difficulty of the mission is the fact that the system is uncharted – good radio show, by the way, Uncharted ! -, so O’Brien decides it is time to chart it.
Bashir sees that the phenomenon that revived Opaka is the same in the prisoners who came back to life. Somehow, the transformation has kept them from dying. Shel-la admits that he has “died” many times before. Bashir wants to get the runabout’s computer working to figure this out, but Sisko says it’s too dangerous. Shel-la wants the answer himself, so he guarantees his protection and Bashir leaves with two of his men.
Opaka questions Shel-la on why the war started, but it’s clear they don’t care, they still want vengeance. It appears that they were sent to the moon as an example for the rest of the population on what happens when two sides can’t come to a peace. The whole moon was designed to prolong their suffering. Kira, needing a defensible area, questions Shel-la about the Ennis’ lack of defenses. He responds that since both sides have realized that they cannot die, their tactics have changed. Sisko suggests that a Starfleet rescue team might be able to transport both of the factions to different planets, where they could live separately instead of continuing their endless fight. He challenges Shel-la to talk to the other leader to get a truce in the meantime.
Meanwhile, O’Brien and Dax find that they can’t trust their sensors due to delta radiation. They’ll need to search one planet at a time, but O’Brien comes up with a design for a differential magnetometer which, fitted onto a probe, should detect the particular magnetic resonance traces in the Yangtzee Kiang‘s hull. This should speed up the search, though Dax is skeptical. Eventually, it works and they are headed to the moon where Cisco’s runabout crashed.
The Ennis and the Nol-Ennis agree to meet at a neutral site near the runabout. Sisko leaves with them, but Kira stays behind with Opaka. Once the others are gone, Opaka starts a conversation with Kira about her [possibly seeing herself] in these hardened people, having fought for so long and delivered so much violence. Kira initially doesn’t see the parallels, but Opaka detects the guilt Kira feels for the violence she committed during the Occupation of Bajor. She says Kira must accept the violence within her in order to overcome the guilt, and comforts her. Kira admits she is afraid the Prophets won’t forgive her for what she has done, but Opaka says they are simply waiting for her to forgive herself.
Bashir returns to the runabout, protected by the Ennis, to repair the computers so that he can investigate the artificial microbes, or nanites, further. He is successful and starts the computer to analyze the data. Soon, Sisko and the Ennis arrive. The Nol-Ennis leader, Zlangco, steps up to them and Sisko explains the deal. Unfortunately, neither side takes the negotiations seriously and the fighting breaks out again, with the Starfleet crew caught in the middle of it. Bashir pushes Sisko out of the way of a weapon that was coming towards him, saying that they can’t afford to die on the moon, not even once.
Dax finds Human life signs on the moon, but O’Brien, upon seeing the satellite system, realizes that it must be using a dampening field to block the Yangtzee Kiang‘s transponder signal, the reason he wasn’t detecting it before. They retreat to a safe distance and he works on getting a communication through.
Bashir explains to Sisko that the biomechanical devices that bring the Ennis and the Nol-Ennis back to life cannot survive in any other environment besides that of the moon. Furthermore, once a person has died with them, the body becomes dependent on them, meaning none of the Ennis or Nol-Ennis, nor Kai Opaka, can ever leave again. O’Brien then cuts in to signal Sisko, and lets him know he’s working on a plan for transport. The satellites are going to make it difficult, though.
Sisko goes to inform Opaka of her fate. However, before he gets to it, Opaka declares she is staying. With a moment of clarity, she believes that she has found the answers to her own prophecies. She says that, even as they came through the wormhole, she sensed that she would not return. She asks Kira to tell the others that she has answered the call of the Prophets, and that she was brought there because it is time for the people on the planet to begin their healing process, just as Kira was brought there to begin hers.
O’Brien manages to find a way to beam the marooned crew away by distracting one of the satellites with a probe, thereby creating a hole in the defense grid established by the satellites.
Meanwhile, Bashir suggests finding a way to reprogram the microbes so that they would stop functioning after death, allowing the inhabitants to die for good and end their torture. However, when Shel-la expresses his intent to use it in order to defeat the Nol-Ennis for good, Bashir disappointingly abandons the idea.
Fighting erupts outside and Shel-la is reluctantly drawn away. Sisko begins to tell the Kai that if they ever find a way to get her off the planet without killing her, they will return, but Opaka interrupts him and tells him that her work is now on the moon. However, her and Sisko’s pagh will cross again. The crew are beamed up, leaving the warring Ennis and Nol-Ennis behind, and the Kai with a lot of work to do.