Bareil stands shirtless in his guest quarters on Deep Space 9 gazing at the stars, when Kira wishes him good morning as she embraces him from behind. He remarks that he thought she would sleep until noon after which Kira reminds him he is supposed to be relaxing. He reassures here he is very relaxed and asks how she is feeling. She claims she is miserable because she wishes he could stay longer; after pretending to consider the issue for a moment, Bareil declares that he will do so for a few more days. However, the election of the Bajoran Kai is at hand — an election Kira is sure Bareil will win. After all, it is common knowledge that Bareil was Kai Opaka's hand-picked successor.
Hearing Opaka's name seems to weigh on Bareil's mind. He reassures Kira that he can never replace Opaka, for without Opaka, Bajor would not have survived the occupation. Whatever is on his mind, it is lost on Kira. As she embraces Bareil, she realizes that the two of them will not have nearly as much time together once he becomes Kai. Bareil reassures her that he will always make time for her, although he acknowledges that doing so will not always be easy and promises Kira he will never lose her.
On the Promenade, Vedek Winn finishes talking to a group of young children, telling them, "Honor the Prophets and they will love you," as Bareil and Kira approach. Bareil politely reminds Winn that the prophets' love is unconditional and they ask for nothing in return. Winn thanks him, with equal politeness, for reminding her how easily the sacred texts can be misinterpreted. The tension between the two of them is evident as Winn remarks that she was unaware of Bareil's presence on the station but, on observing Kira, adds that she is not surprised. Bareil claims he would not try to surprise her and Winn notes that she has been watching him closely. Winn sees nothing wrong with this, as the eyes of all of Bajor are on the expected future Kai.
Kira jumps in on hearing this and eagerly asks if Winn is announcing her intention to concede the race for Kai. Winn however points out that the Choosing is still two days away and the Prophets may still have a surprise in store. Kira suspiciously asks what the purpose of Winn's visit is to be, but Winn politely responds that had she wanted Kira to know she would come, she would have told her. In any case, Kira plans to warn Constable Odo to increase station security. When Winn reassures Kira that she believes she will be quite safe, Kira counters by clarifying that the extra security is not for Winn's protection. An indignant Winn asks what Kira is implying, but Bareil reassures her it was nothing. Knowing when to back down, Kira agrees that her comment was innocent. Winn acknowledges Kira's belief that she orchestrated the attempt on Bareil's life the year before, but she says she prays the Major will "be cured of this unfortunate misconception" — a prayer Kira reassures Winn will never be answered.
Meanwhile, an elderly Bajoran man walks along the Promenade. Another Bajoran, Eblan, bumps into him and apologizes for the mistake before looking back with recognition. He gently grabs the older man's arm, identifying him as Kubus Oak, a traitor who worked for the Cardassians during the occupation. Kubus angrily tries to get past the younger man, but the man announces Kubus' identity to the entire Promenade. Odo intervenes as a crowd begins to form and asks what is going on; upon seeing Kubus, Odo recognizes him immediately. Odo claims he was under the impression Kubus was living on Cardassia, but Kubus says he has decided to return home. "Welcome back," Odo greets him sarcastically. "You're under arrest." As Odo escorts Kubus to the security office, he seems to recognize Vedek Winn, who has observed the incident intently.
In another orb experience, a group of Vedeks is gathered on Bajor as Bareil, newly elected Kai of Bajor, emerges from a nearby doorway. "The prophets have spoken!" proclaims Winn. "All blessings on the new Kai!" The other Vedeks echo her sentiments in unity, chanting a blessing to Bareil. Bareil seems pleased if somewhat unsure of himself until Kai Opaka appears in a flash of light. Opaka tells him he must be strong now more than ever. Bareil asks why Opaka left him, to which she tells him all is as the prophets will it to be and asks him to follow her. Before he can do so, Winn warns him that Opaka's path is a narrow one. Although Bareil does not believe he deserves to walk in Opaka's path, Opaka warns him that such is his destiny. He walks toward her slowly as Prylar Bek approaches carrying a small, round box. Telling Bareil the box is a gift from the prophets, he opens it to reveal a venomous snake. Bareil hesitates shortly, but Opaka assures him the snake's venom will make him strong. He removes the snake to find a noose, and as he does so, the orb experience ends.
Secretary Kubus sits in a holding cell as Odo informs him that extra security was needed to prevent a mob from forming outside. Kubus tells him he always was good at his job, Odo counters by pointing out that Kubus was equally skilled at his job as the liaison officer between the Cardassian forces and the "government" of Bajor. Defending his actions, Kubus claims that the situation on Bajor would have been ten times as bad if he and the other officials had not cooperated with the Cardassians. However, Odo fails to see how Kubus, who spent most of his time aboard Terok Nor, would know. Although Kubus claims he could not stand Gul Dukat, describing Dukat as an arrogant tyrant, Odo reminds him that Dukat once described Kubus as his favorite Bajoran. Obviously burdened by the weight of his actions, Kubus admits that he should never have left Bajor.
"But you did," says Major Kira as she interrupts their conversation. "And you're going to have to live with that decision." Odo introduces Kira as the highest-ranking Bajoran on the station, and when Kubus requests an audience, she tells him to make it quick as she does not enjoy talking to collaborators. Kubus asks that he be allowed to return home, a request Kira denies. The Ilvian Proclamation exiled all Bajorans who were part of the Bajoran occupational government, and Kubus' name was fourth on that list. Kira adds that she personally believes that Kubus and the others got off too easily. Kubus pleads with Kira, seeing no harm in allowing him to live out his few remaining years on Bajor. On hearing this, Kira angrily confronts Kubus with the fact that his signature was on numerous work orders, which were essentially death sentences, forcing Bajorans to mine ore for the Cardassians. As such, allowing him to return to Bajor would dishonor the memory of every Bajoran who died working in the mines.
Vedek Winn visits Commander Sisko in his office to inform him with some hesitance that some on Bajor believe the relationship between the two of them is "not all it should be." According to Winn, she finds such inaccurate perceptions to be most disturbing. Sisko coldly asks whether such perceptions are inaccurate, although Winn does not seem to think there is any reason for Sisko to believe otherwise. Sisko points out that Winn once claimed he was sent to destroy Bajor. In an attempt to downplay this point, Winn explains that she only meant Sisko was sent to test the faith of the Bajoran people, although she concedes that she was concerned about Bajor's petition for Federation membership. However, when Sisko asks directly whether Winn now supports the petition, Winn simply replies that she will not oppose the will of the prophets. Sisko requests that Winn tells the same to Bajor, so she suggests a joint appearance. Although Sisko knows she is attempting to garner support for her bid to become Kai, he agrees — suggesting an appearance the following week. Winn benignly asks why they should wait, as the Vedek Assembly would allow them an immediate audience if the Emissary requested it. Sisko points out the obvious: that such an appearance now could be construed as support for Winn, and as a Federation officer, he is not permitted to interfere in Bajoran affairs. "What an enlightened philosophy," Winn replies. They both agree to an appearance the following week, although it is unclear whether either intends to follow through on it.
Odo interrupts Kira to inform her that Secretary Kubus is about to leave for Bajor, because Winn has granted him sanctuary. Kira immediately contacts Dax, who is about to clear Winn's ship for departure, and tells her not to release the docking clamps. Proceeding to the security office, Kira learns that Winn spent approximately ten minutes talking with Kubus before requesting the use of Odo's computer to access the library system. Although Odo is unsure of what Winn looked up, she proceeded to contact the Bajoran provisional government and informed them of her intent to grant Kubus sanctuary. They discover that Winn requested information on Prylar Bek, the liaison between the Vedek Assembly and the Cardassian occupational forces and a known associate of Kubus. On a hunch, Kira tells Odo to check whether Winn accessed information on the Kendra Valley Massacre, which she did. Odo suggests that perhaps Kubus told Winn something new about the massacre, but Kira is not sure what could be new; in the massacre, 42 Bajoran Resistance members died, including Kai Opaka's son, because Bek gave the Cardassians the location of their cell. Bek later hanged himself, detailing what he had done in his suicide note. As Kira is explaining this, Winn enters the office.
Asking to speak with Kira in private, Winn confronts her about detaining her ship and "suggests" that Kira allow her to depart immediately. Kira, who knows she cannot legally detain Winn, assures the Vedek that she is free to go, but informs her that, in light of public sentiment toward Kubus, no ship carrying him can be allowed to depart without a thorough security sweep — including scans for nanotechnology, which could take days. Both of them know the real reason for Kira's scans, so Winn reveals to Kira that in exchange for sanctuary, Kubus has agreed to give her the name of the man responsible for the Kendra Valley Massacre. It is common knowledge that Prylar Bek revealed the location of the encampment, but Winn informs Kira that Vedek Bareil ordered him to do so.
Outraged at Winn's accusation, Kira warns her that no one will believe the word of a convicted traitor such as Kubus. However, Winn tells her that she never claimed to believe him; she simply wants to protect the sanctity of the Bajoran faith. Winn claims her intention is not to grab power but to protect Bajor, for as adamant as Kira is that Bareil is not a collaborator, were he elected Kai and later revealed to be one, Bajor would be devastated. While Winn has not yet condemned Bareil, she did not know who to trust with such a delicate investigation until now; however, she believes Kira is the perfect choice. Kira begrudgingly agrees to conduct the investigation so long as Winn promises not to make the allegation public until it has concluded. In exchange, Kira promises to give Winn her findings, whatever they may be.
Kira, Winn, and Kubus are gathered in a cargo bay when Kira asks Kubus if, during his association with Prylar Bek, he knew the man was a collaborator. Kubus insists that Bek was not a collaborator, only a messenger between the Cardassians and the Vedek Assembly. In the weeks prior to Bek's suicide, Kubus observed that he had become erratic and was in constant communication with a then-unknown source within the Assembly. The day after the massacre. However, Vedek Bareil visited Bek for several hours, during which time Kubus could hear shouting coming from Bek's quarters. Bek hanged himself on the Promenade shortly thereafter. Based on this, Kubus believes that Bek wanted to confess his betrayal but Bareil forbid him to do so which led to his suicide, a theory Kira regards as incredible. There could be a dozen explanations for Bareil's contact with Bek — and as Winn points out it is Kira's job to find which of them is true.
Visibly troubled, Kira contacts Bareil, who admits coming to the station to meet with Bek on the day in question. While he denies any involvement in the massacre and seems sure Winn will not be able to prove anything, Bareil cannot reveal what he and Bek talked about due to confidentiality between monks and their Vedeks. She solicits Odo's help, but as the Cardassians removed all communications logs on their withdrawal from Bajor, Odo must establish a link with the Bajoran Central Archives. As he does so, he observes how troubled Kira is; while she insists that she knows Bareil is not guilty, she admits she is still afraid he might be.
Kira is deep in thought as Odo contacts the Bajoran Central Archives. After a few seconds, she admits to both Odo and herself that she loves Bareil. As she says this, a pained look appears on Odo's surprised face, although Kira is facing the wall pensively and fails to notice. He stutters with his response and Kira turns to him, wondering if something is wrong, but he covers his true feelings with one of his usual observations on the frivolity of humanoid relationships. "I was just wondering when you were going to figure that out," he explains of her feelings for Bareil. Once Odo accesses the archives, he discovers that the records between Prylar Bek and the Assembly for the week prior to the Kendra Valley Massacre have been sealed. However, he is not able to determine who sealed the records, only that there is a security seal present. One thing is certain: Only a Vedek could have placed the seal there.
Kira and Odo visit Quark's, against Kira's better judgment, where they find the Ferengi entrepreneur paying one of his Dabo girls. As Quark counts out ten strips of latinum, the busty woman gives him a look and he is forced to add four more, after which she kisses his bald forehead and walks off. "I hate payday," he comments to himself before he realizes Kira and Odo are standing behind him. Grasping his latinum container, Quark says, "Whatever she told you, I didn't do it." The two of them take perverse pleasure in Quark's visible discomfort at seeing them. When Odo tells Quark to relax, the Ferengi claims to have developed a persecution complex because of them, asking what they want and how much trouble it will cause him. Kira reassures him that they only want him to break a security seal and it will cause no trouble at all, to which Quark asks in a rhetorically innocent tone, "Isn't that illegal?" He refuses to help them and cites the 285th Rule of Acquisition: "No good deed goes unpunished." On hearing this, Odo grabs Quark by the shoulders and leads him over to the computer terminal behind the bar with an air of sibling rivalry. Quark removes a panel on the computer as Odo tells him he can gain access to the Vedek Assembly files via the Central Archives, a strategy Quark dismisses as amateurish. As he inserts a data rod into the computer and begins to configure it, Odo leans in to observe. Giving the Changeling an indignant look, Quark grabs Odo by the shoulders and escorts him from behind the bar, shooing both him and Kira away.
Outside Quark's, Odo brings Kira to the spot where Bek hanged himself, observing that, while he did not know Bek well, he thought he was a good man. Kira points out good men do not betray their own people, but Odo tells her that given the fact of extreme circumstances, even the best humanoids are capable of committing horrible acts. Quark interrupts their conversation as he gestures them over to announce that he was able to break through the security seal. However, upon doing so, he discovered the files in question were empty as someone had erased all of the message logs.
Chief O'Brien helps Kira search for a way to retrieve the lost data contained in the erased logs. While data is still stored in the computer memory after deletion, the data fragments could hypothetically be unscrambled and pieced together. He warns her that to do so would take more time than they have. However, he thinks he might at least be able to pinpoint who erased the information. The accompanying retinal scan was deleted along with the logs, but like the logs, it is possible to piece the scan together from data fragments. Kira is obviously lost as he shows her the mathematical representation of the data fragments while the computer attempts to form an image. After O'Brien finishes, the computer finds a match and fills in the missing pieces of the retinal scan to reveal who erased the logs: Vedek Bareil.
Bareil has an another orb experience, in which he revisits the image of his inauguration as Kai. His vision flashes back to the Bajoran temple aboard DS9, where Bek confronts him accusingly. "You!" the Prylar exclaims. "I trusted you. I needed you. You let me die."
Now Bareil is in his quarters just as he was earlier, with Kira's arms again embracing him from behind. He turns around to kiss her, only to discover he has kissed a naked Vedek Winn. With a grin, she tells him he will be rewarded.
He suddenly finds himself on Bajor as Kira comes toward him seductively, claiming she has a gift from the prophets. Bareil seems cautiously yet pleasantly surprised, but as she is closing in, she stabs him in the stomach. As he collapses, Kai Opaka catches him. "May the prophets comfort you, my child," Opaka tells him softly. "May they comfort us all." Kira and Opaka watch as Bareil loses consciousness and awakens from the orb experience, as there is a knock on his door.
It is Kira, who is obviously in pain and has come to find the truth. The truth, Bareil concedes, is not always easy to recognize. Kira tells him that she recognizes it, but she does not like what she sees, desperately asking why he erased the transmission records. "Please, don't make me do this," Bareil begs her, but she sees no other choice. She still seems to maintain some hope that Bareil is innocent, confronting him with the charges against him: ordering Bek to reveal the location of the base, thereby killing forthy-three Bajorans, including Kai Opaka's son. On hearing this, Bareil turns away and relates how the Cardassians were determined to wipe out the resistance in the Kendra Valley, being prepared to kill 1200 innocent Bajorans in the area; he felt he had no choice. Kira, near tears, says Winn will destroy him now, but he corrects her: He has destroyed himself.
Solemnly entering Ops, Kira asks for a status report and O'Brien tells her everything is under control. Dax reports that Kai Winn is waiting for her on an urgent subspace frequency, and as she already knows what the message is about, Kira accepts it in Ops. Kai Winn has been waiting for a response, but before Kira can say anything, Winn congratulates her on a job well done. She already knows the result, as Bareil has made a surprise announcement in which he withdrew himself from the Bajoran Choosing Ceremony. Acknowledging Kira's pain, Winn reassures her that what she did was for the good of Bajor and adds, "Whoever is chosen tomorrow to be the new Kai will owe you a debt of gratitude." As she realizes the ramifications of Bareil's actions, Kira seems to be deep in thought. Dax asks if she is all right, but Kira points out that the scenario does not make sense. Soliciting O'Brien's help, she accesses the Vedek Assembly archives once more.
Back on Bajor, while the Vedek Assembly performs the choosing ceremony, Kira waits outside impatiently, already knowing how it will end. A number of Vedeks exit the building, followed by a pair of Prylars escorting Kai Winn. Grasping Kira's ear, Winn says Kira's pagh is strong and reassures her that, in time, she will no longer see her as an enemy. "I hope that's true," Kira says solemnly. "I know you do," Winn replies, adding that she must postpone her planned appearance with the Emissary, at least for now. She walks away as the rest of the Vedeks exit the building.
Once the crowd has cleared, Vedek Bareil emerges, surprised to see Kira. Having finally discovered the truth, Kira reveals that in his quest to purge the evidence of after the massacre, Bareil forgot about the transit files. He is unsure of what she means, so Kira tells him that transit files for the time surrounding the Kendra Valley Massacre prove he was not a collaborator. During the time in question, Bareil was on a personal retreat at the Dakeen Monastery during which time he had contact with virtually no one. She has even verified the transmissions log from the monastery and confirmed that the sole transmission was an incoming one recalling Bareil to Bajor after the incident. Thus, without any doubt, Bareil could not be the traitor. He tries to stop her as she speaks, but Kira refuses to be silenced.
The real traitor had to have been someone dear to Bareil — someone more important than Kira herself or his desire to become Kai. Bareil pleads with her as she continues, but as they both know what she is talking about, Kira sees no reason not to say it. The only person that dear to Bareil was Kai Opaka herself. As Kira speaks, Bareil looks down at his feet. Opaka logically knew where the base was located because her son was a member of that resistance cell. She sacrificed him and 42 other Resistance members to save the lives of 1200 people. "So," Kira says, "Now we have Winn to lead us." Taking on a tone mockingly reminiscent of that which Winn often uses, Bareil replies, "It is the will of the prophets." Kira wonders where Winn will lead the Bajoran people, and Bareil admits that the future is uncertain. Watever the future holds in store, Winn will need their help. When Kira asks what this means for her relationship with Bareil, he counters by asking where she wants it to go. She replies by embracing him, and after a few brief kisses, the two of them walk away together.