While giving a lecture on the wormhole, Keiko receives a rather obtrusive visitor: Vedek Winn, a Bajoran religious bigshot, and potential candidate to take Opaka's recently vacated position of Kai. Vedek Winn is there with a complaint: She wants the religious teachings of the Prophets taught in Keiko's class. And she's not at all polite about it.
Keiko is understandably peeved about Winn trying to run rough-shod over what she can and can't teach. Kira on the other hands supports Winn, noting this is a Bajoran station. Sisko is stuck in the middle, trying to keep a lid on the situation.
Miles meanwhile has been feeling off lately. One of his tools has gone missing, and his assistant Neela seems to be doing all the work. And to top it off, Ensign Aquino has failed to report for duty. Well, Miles and Neela find him...as a gray bit of sludge in a plasma conduit. All signs point to an accident. But O'Brien isn't convinced.
Winn's message meanwhile has been spreading throughout the station. Bajoran vendors refuse to sell to Starfleet members, and Winn has gotten all the parents to pull their children out of school. With the threat of her classroom being emptied of all but five students, Winn suggests a "compromise". Keiko doesn't have to teach their spiritual beliefs...she just has to stop teaching about the Wormhole altogether. Keiko naturally tells her to stuff it. And so, the parents take their kids away.
Sisko seeks some advice on Bajor by visiting Vedek Bareil, the Vedek challenging Winn for Kai, and winning from the sound of it. Bareil wants to help, but he knows politics. He knows supporting Sisko at this time could sink his chances for Kai. And tells Sisko he'd love to help... if he makes Kai.
Back on the station, Aquino's "Accidental" death isn't holding water. He was incinerated at 4:00 AM. Despite his last log entry, his turbolift log traces him to one of the runabout pads, nowhere near the plasma conduit where he was found. And Bashir poking around reveals he wasn't killed in the conduit. He was already dead when incinerated, by a phaser set on kill.
Meanwhile, Odo observes the growing presence of Bajoran fundamentalists coming onto the station. After questioning Quark on his knowledge of the incident, the constable is presented with new evidence by Miles: Evidence of tampering was discovered at Runabout Pad A. The issue being Aquino's body was discovered on Pad C. Odo deduces that the murderer was trying to procure a Runabout, was discovered by the unfortunate Aquino, and killed him. As they discuss it, a massive explosion rocks the promenade.
The (thankfully empty) school has gone up in flames. With the incident, Vedek Winn tries rallying the Bajoran residents against Sisko. But Sisko shuts her down hard.
O'Brien meanwhile is closing in on the killer of Aquino. Doing a bit of digging, he finds the weapons sensors on the promenade have been deactivated, but fiddled with to appear active. Just in time for Vedek Bareil to arrive on the station after hearing news of the bombing. And there's only one person with the skill to do this: Neela.
Indeed, Neela is among the crowd there to greet Vedek Bareil when he arrives. O'Brien manages to get word to Sisko in time, and foils Neela when she tries shooting Vedek Bareil. Neela was working for Vedek Winn, intending to assassinate him and eliminate her competition for Kai.
Unfortunately, Neela claims she worked alone. And Winn gets away with attempted murder. Afterwards, Kira is sulking on the bridge. She's distraught that Winn is nothing but a power-hungry crook. But she finds a bright side. Noting how at this time a year ago, she was a freedom fighter with no real direction. Now, she's working with Sisko on a space station protecting her home. Progress is a blessing in and of itself.
- Kira: "I don't think that you're the devil."Sisko: "Maybe we have made some progress after all."
And with that, season one ends.
- Arbitrary Skepticism: Sisko, maintaining a moderate perspective on the issue, makes the point that since the Prophets are Sufficiently Advanced Aliens that have used their extraordinary abilities and nigh-omniscience to foster with Bajoran history, that calling them gods isn't so far-fetched. When Jake questions him further on it, he clarifies his point - that regardless of whether one believes in the Bajoran religion or not, the Bajorans shouldn't be thought less of for having it.
- Artistic License History: Keiko, in an obvious fit of pique and ego, changes her lesson plan to teach about Galileo striving to preach the truth of heliocentrism against the awful persecution of church doctrine (not-so-subtly drawing a comparison between the famous scientific martyr and herself). Except that Galileo 1) wasn't the first to venture the idea of heliocentrism, 2) actually denied really believing in heliocentrism when pressed by the church, and 3) the church largely treated him with kid gloves due to his age, infirmity, and the fact that he cooperated with them willingly the entire time. Additionally, the church wasn't dead set against heliocentrism (Copernicus, who developed the theory, was a Catholic priest after all), and a number of Galileo's detractors came from within the scientific establishment (heliocentrism would overturn 1,500 years of established science dating back to Claudius Ptolemy). Moreover, it was an attempt to reinterpret The Bible, as well as mockery of the Pope, that really got Galileo in hot water with the church. A better example would have been the Scopes trial.
- Big "NO!": Sisko while stopping Neela from killing Bareil.
- Bitch in Sheep's Clothing: Neela, who was introduced as a helpful and eager junior engineer. Too bad about that whole "fanatic assassin" thing.
- Corrupt Church: Vedek Winn uses her position as a religious leader to manipulate herself into gaining more power, influencing one of her followers to kill a rival so that she can take his influence in their order. Due to her true goals, how much she even believes in what she preaches is questionable.
- As it becomes increasingly clear that she wasn't operating in good faith over the course of the episode and Sisko and Bareil add their voices to the debate, it becomes obvious that her objections don't even make sense by her faith's internal logic. Nobody is challenging anyone's beliefs, because everyone agrees on the core facts; her whole criticism is the use of neutral words instead of religiously charged ones.
- Curse Cut Short: Keiko stopping Miles from telling a rude Bajoran salesman where he can stick one of his jumja sticks.
- Does This Remind You of Anything?: The debate between Keiko and Winn is a rather direct parallel for the debate between evolution and creationism in America. (Sisko also points out parallels to heliocentrism and Galileo.) In particular, the episode (through Sisko) makes the point that the real issue is cultivating conflict and antagonism between perspectives, and in true Star Trek fashion posits that in an ideal world all perspectives should be considered equally valid. The comparison does fall apart when you realize the debate in the episode boils down mostly to word choice: the "non-believers" readily acknowledge that the Wormhole Aliens are the Prophets of Bajoran religion (although Keiko does seem reluctant to acknowledge that "Prophets" could be a valid term for beings who can see the future).
- Don't Call Me "Sir": Sisko's reaction to Vedek Winn calling him "Emissary":Sisko: I wish you wouldn't call me that. I'm "Commander Sisko." Or "Benjamin," if you'd prefer.
- Establishing Character Moment:
- Vedek Winn walks into Keiko's classroom and quickly accuses her of blasphemy.
- Vedek Bareil dispenses with the practice of cupping Sisko's ear when they first meet on Bajor, a traditional greeting by Bajoran holy figures. This act impresses Sisko, who confesses it makes him uncomfortable, to which Bareil wholeheartedly agrees (which helps establish Bareil's moderate position compared to the much more fanatical Winn). Notably, when Vedek Winn tries to greet Bareil in this manner after his arrival on DS9, Bareil can be seen intercepting her and clasping her hand.
- Found the Killer, Lost the Murderer: Sorta. Sisko apprehends Neela before she can kill Bareil, and both Sisko and Kira know damn well that Winn is pulling her strings. Unfortunately, they have no hard evidence, and Neela claims that she acted alone, so Winn gets away.
- Foil: Vedek Bareil and Winn representing the moderate and extremist arms of the Bajoran religion.
- Heel Realization: Early in the episode, Kira supports Winn and her orthodox views. After the assassination attempt on Bareil, she gives it a serious rethink.
- The Informant: Quark would gladly sell out any of the killers he knows if he could, but he knows that none of them were responsible for Aquino's death.
- Karma Houdini: Vedek Winn gets away with planning to murder Vedek Bareil, due to Neela claiming she acted alone. Though her chances for Kai appear to be shot. Or not...
- Madness Mantra: "The Prophets spoke! I answered their call!"
- Magic Versus Science: Discussed. Keiko's teachings of the wormhole are secular in nature, with the Prophets referred to as "wormhole aliens" or "entities". Winn takes umbrage with these teachings, declaring them blasphemy, and tries to force Keiko to teach her students about the wormhole through a lens of spirituality, or else force her to quit teaching altogether. Sisko suggests that Both Sides Have a Point, and it's not for him to say who's right and who's wrong. It's muddled by the fact that Winn's faction is considered somewhat extremist even by her religion's own standards; Bariel and his faction think her objections are just stupid.
- Make It Look Like an Accident: Neela tried to cover her tracks by altering Aquino's log to make it appear like he was going to repair a faulty power conduit where he was found. However, she didn't or couldn't alter his turbolift record, which tracked him to the runabout pad where he was actually killed.
- Manipulative Bastard: Vedek Winn. She cultivates a religious conflict on the station simply so Sisko will reach out to another religious leader to help fix it, all so she can use the opportunity to kill the other leader once the situation gets so bad that he visits Deep Space 9 personally. She not only manipulates Sisko and Bariel, she covertly sabotages key systems on the station to facilitate her plans: if not for O'Brien noticing a missing tool from his toolbox, she might have succeeded. Either way, she gets off scot-free.
- Passive-Aggressive Kombat: Vedek Winn is a clear master of this, mixing insincere apologies, unreasonable demands and back-handed compliments.
- Patrick Stewart Speech: Mixed in with a good dose of "The Reason You Suck" Speech, when Sisko verbally bitch-smacks Winn.Sisko: The Bajorans who have lived with us on the station, who have worked with us for months, who helped us move this station to protect the wormhole, who joined us to explore the Gamma Quadrant, who have begun to build the future of Bajor with us, these people know that we are neither the enemy nor the devil. We don't always agree. We have some damned good fights in fact, but we always come away from them with a little better understanding and appreciation of each other. You won't succeed here. The school will reopen. And when your rhetoric gets old, the Bajoran parents will bring their children back.
Winn: We will see.
- Reassigned to Antarctica: Threatened by Sisko when several Bajorans fail to show up for duty claiming "illness". He says they better have a miraculous recovery, or they can get better on their way to their next post.
- Red Shirt: Poor Ensign Aquino. Never even got to be alive onscreen.
- Rule of Three: Bareil explaining to Sisko why the Vedek Assembly will not meet with him:"Some fear you as the representative of a Federation they view as godless. Some fear you as the Emissary who walked with the Prophets. And some fear you because Vedek Winn told them to."
- Sure, Let's Go with That: Vedek Bareil "accepting" Sisko's invitation to tour the station.