It is a regular morning aboard Deep Space 9 with Keiko O’Brien heading to school as Chief O’Brien heads to work. The two discuss the sweet taste of a jumja stick while walking the Promenade, and Miles’s Bajoran assistant Neela. Later, Keiko begins teaching the children about the Bajoran wormhole. As the lesson begins, a Bajoran religious leader by the name of Vedek Winn suddenly enters the classroom and asks Keiko to continue. Keiko continues to talk about the wormhole in a scientific way; however, Winn argues against the lesson telling Keiko the wormhole is actually the Celestial Temple and the entities living there are the Prophets. Keiko explains that while she appreciates the Bajorans believe these things, she is teaching the children science and not spiritual beliefs. Winn tells Keiko that what she is doing is teaching blasphemy, and warns that she will not allow her to continue.
O’Brien is late arriving to supervise Neela in fixing a junction in Odo‘s security office, but she has already completed it and is ready to test. O’Brien tests it, and is impressed, ready to close the panel. However, he is missing his EJ7 interlock from his case. He’ll have to find it.
Winn immediately starts to gain support among the Bajoran civilians who live on the station, while Keiko goes to meet with Commander Sisko. Sisko admits that he always felt this situation was going to crop up eventually, and admits he sometimes wonders if they can find the common ground needed to help ensure Bajor’s admission into the Federation. He asks Kira to join the meeting, and asks her about Winn. Kira explains that Winn is a member of an orthodox Bajoran religious order who is currently in the running to take-up the vacant post of Kai, although she isn’t expected to succeed.
Kira then admits that she supports both Winn’s candidacy as well as her viewpoint regarding teachings about the wormhole and asks Keiko if she would be willing to revise the school curriculum or consider having a separate school for Bajoran children, but Keiko outright rejects both ideas. Sisko suggests that Keiko teach the spiritual beliefs surrounding the wormhole in addition to her current lesson plan, but Kira reminds him that there are two completely different philosophies at the center of the debate. Keiko argues that she isn’t trying to teach any philosophy, but Kira states that choosing to talk about the wormhole from a purely scientific point of view is a philosophy in itself. She’s unsure if the situation can be resolved.
Commander Sisko decides to go visit Vedek Winn while she is at the Bajoran Shrine, however he is made uncomfortable when she addresses him as the Emissary of the Prophets. He asks her not to call him that, but she tells him he has taken up a deeply important role in the Bajoran faith, and how she was punished by Kai Opaka when she questioned why a non-believer was the one to find the Prophets when she (Winn) would have done anything to meet them. Wishing to get to the heart of the matter, Sisko asks Winn if she is willing to discuss her issues with the school, but Winn tells Sisko that she is acting on behalf of the Prophets and that there will be serious consequences if Keiko does not back down from her position.
In Ops, O’Brien is determined to find the tool he is missing, as it could be used to access critical systems. Lieutenant Dax then reports that Ensign Aquino, an engineer, failed to report for duty, so they try to use the computer to locate the tool by looking for tritanium. In a maintenance tunnel on Level 12, Section 8, Neela finds a blob of sludge in a power conduit, and a subsequent analysis by Dr. Bashir reveals that it is the remains of both Ensign Aquino and the EJ7 interlock. They had apparently been incinerated by a power surge while Aquino worked on the power conduit at 4 AM that morning.
As O’Brien is walking Keiko to school, he stops at a stand for his usual morning jumja stick, but the Bajoran vendor refuses to sell him one, because of the current controversy involving Keiko. Keiko moves Miles away from the vendor before he attacks him and they move on to the schoolhouse, where they meet Vedek Winn outside the school. She has gathered a group of Bajoran parents and children.
Vedek Winn attempts to negotiate in public: she will not object to Keiko teaching a non-spiritual viewpoint of the Wormhole, if Keiko simply does not teach about the Wormhole at all.
Keiko replies that it is her job to open children’s minds to knowledge, not to hide it from them. Keiko asks if Vedek Winn will also object to teaching of evolution, and of the origin of the universe. Winn leaves with the Bajoran contingent, officially boycotting the school. Finally, only five of her students remain including Jake Sisko.
The senior staff is assembled to discuss Aquino’s death. O’Brien gives a plausible theory, except he doesn’t believe Aquino took his tool without asking, and the repair could have waited. It’s an odd situation. Sisko suggests Odo look into it.
After the meeting, Jake Sisko tells his father about school. Keiko continues to teach her remaining five students about Galileo, and how he was tried by the Inquisition for his belief that Earth revolved around the Sun.
Jake makes the connection between the story of Galileo and current events on the station. He tells his father that the current controversy is stupid, and asks where the Bajorans get such ideas. Commander Sisko, however, points out that the Bajoran religion is quite reasonable in light of the Wormhole and the nature of the Prophets, and counsels Jake to be tolerant of the beliefs of other cultures. Or else, he warns his son, he will be acting just like Vedek Winn – seeing an issue from only one side.
Sisko, attempting to heal the rift between Starfleet and the Bajorans on Deep Space 9, travels to the planet to meet with Vedek Bareil, the favored candidate to replace Opaka as Kai. Unlike Winn, Bareil is forward-thinking and personable however he is unwilling to arrange an audience for Sisko with the Vedek Assembly since being seen to ally himself with the Federation will certainly harm his chances of being elected. Bareil promises that if he is elected Kai, he will be able to show friendship then but right now can do nothing to help.
Upon returning to the station, Sisko is angry to find that three Bajoran crewmembers have refused to report for duty. He asks Kira for her opinion, and she tells him that as far as she’s concerned the only reason the Bajoran government haven’t asked the Federation to leave is because if they do the Cardassians will certainly return to retake Bajor and claim the wormhole. Sisko, angered that all his apparent efforts to bridge the gulf with the Bajorans over the past several months have fallen short, orders Kira to get the Bajorans back to work immediately or they will be reassigned.
Further analysis of Ensign Aquino’s remains by Dr. Bashir reveals that Aquino was not killed by the discharge in the power conduit. Instead, Aquino had already been killed by phaser fire.
In Sisko’s office, he wonders to his staff if the murder is related to the school issue, but Aquino was killed before Winn arrived. Furthermore, Odo reports he was actually headed to runabout pad C, not to the power conduit. O’Brien and Neela go to check the runabouts, but Neela reports that she has already performed the diagnostic that O’Brien would have. It appears normal, and so they sit down to think. After a brief chat about how Starfleet and Bajoran officers don’t socialize, Neela says O’Brien is easy to work with since he’s not fake, and compliments him. He dismisses her, thinking about what his wife was saying earlier.
Odo and Quark observe the Promenade sitting in the Replimat as a deputation of Orthodox vedeks arrives on the station, summoned by Winn to support her boycott of the station’s school. Odo asks if Quark knows anything about Aquino’s murder. Quark says he does not but agrees to “keep [his] ears open.“
O’Brien then approaches Odo and says he has found evidence of tampering at Runabout Pad A, but is confused because Pad C, where Aquino’s body was found, was clean. Odo says it makes sense: Aquino surprised his murderer in the act of tampering with Pad C, and after killing him, the murderer switched his plan to Pad A. The tampering seemed intended to allow the murderer to steal a runabout, but none are missing. Odo is confused: “he goes through a lot of trouble to defeat the security net, and then doesn’t go through with his plans.“
Before he can pursue this line of thought further, a bomb goes off in the schoolhouse. O’Brien runs in panic towards the school in fear that Keiko was inside, which is blazing, but thankfully, the school was not in session and no one was hurt.
Sisko and several station personnel go to the school, where they are met by Vedek Winn who asks after Keiko. Sisko, knowing that Winn was likely connected to if not directly responsible for the bombing, tells her that he’s holding her responsible for the recent act of terrorism and informs her of his belief that, since her order is rarely listened to on Bajor she instead began the school issue to gain more support. Winn in response accuses Sisko (and, by extension, the Federation) of wishing to destroy the Bajoran way of life. Sisko denies the accusation and makes an impassioned speech where he speaks of how the Federation and Bajoran people have worked hard together over the last several months, and regardless of if they’re having a discussion or an argument they still come away with a better understanding of each other. He finishes by telling Winn that her attempts to cause trouble won’t succeed, and the Bajorans will eventually bring their children back to school. She simply says “we’ll see” and Sisko leaves. Then, Neela and Winn exchange a look.
Back in Ops, Sisko is contacted by Vedek Bareil, who has heard of the bombing and decided to publicly offer Sisko his support.
In the Bajoran shrine, Neela secretly meets with Vedek Winn and tells her that her plan to escape via runabout has been stopped and she now has no way to escape arrest and possible execution. Winn is uncaring, and orders Neela to proceed with their plan anyway, citing the will of the Prophets.
In Ops, O’Brien discovers a secret file lodged in Deep Space 9’s systems. With Dax’s help, O’Brien decrypts the file (named “ANA”), and discovers that it contains the instructions to disable a series of force fields and create an escape route from the Promenade to one of the runabouts. He immediately locks down all the runabout pads to prevent anyone from using them to escape.
Bareil takes Winn to the school to advocate for a peaceful resolution to the events, and she follows, soon joined by Sisko. As they speak publicly, O’Brien discovers that a security console in Odo’s office has been tampered with. Suspicion immediately falls on Neela, who had repaired the security console several days earlier, and O’Brien realizes that she tampered with the security systems so that a weapon could be smuggled onto the Promenade.
O’Brien contacts Sisko and informs him of his suspicions. Scanning the crowd in front of the school listening to Bareil’s speech, Sisko sees Neela drawing a phaser from her toolbox and aiming at Bareil. He charges through the crowd, which jostles Neela and spoils her first shot. Before she can fire a second, Sisko tackles her to the ground, saving Bareil’s life. Odo drags Neela away, as she yells that “the Prophets spoke” and she “answered their call“.
Kira rounds on Winn, accusing her of orchestrating the entire school controversy just to lure Bareil to the station and have him killed, to stop him from being elected Kai. Winn turns away without responding.
Later, in Ops, Sisko finds Kira in a melancholy mood at her station. He confirms that Neela has refused to incriminate Winn, and Kira says she never will, leaving them with no proof of Winn’s involvement. Kira admits that she supported Winn because Kira wanted her own faith to be as strong as Winn’s was. She also says that she listened to Sisko’s speech on the Promenade when he faced off with Winn, and agrees that she has begun to trust him and the Federation. She adds that she does not think of Sisko as the devil. Sisko smiles, saying Starfleet and the Bajorans have made some progress after all.