As Major Kira and Doctor Bashir make their way back to Deep Space 9, Kira asks Bashir to take control of the runabout, as she has a headache and would like to meditate. Bashir mentions that he once had the opportunity to study with a rhythmic breathing expert named Isam Helewa, but Kira seems less than interested. When he mentions that he would like to learn any Bajoran techniques, Kira tells him that Bajorans usually just sit quietly. There is a brief pause as Kira meditates before Bashir begins breathing sporadically. She looks up, irritated, and asks him what he is doing. He explains that he is using a technique called Bellows Breath meant to increase one's energy flow.
In an attempt to change the subject, Kira suggests that they listen to some music. An undaunted Bashir asks what type the Major prefers, but unfortunately her musical knowledge is limited to Bajoran composers. He immediately tells the computer to play a selection by Tor Jolan, one of Bajor's greatest composers, much to Kira's surprise. She wonders how he knows of Tor and he explains that he has made a point to listen to Bajoran music since he was assigned to DS9. They seem on the verge of finding a common ground when he starts comparing Tor to the great Boldaric masters of the previous century which seems to further anoy Kira. He remains as gung ho as ever, attempting to get to know Kira on a first-name basis.
Bashir goes on to say that Nerys is one of the most interesting women he has ever met and he is glad they are putting past conflicts behind them. Kira sarcastically adds that they are making room for new ones. Laughing, Bashir relates that he and Chief O'Brien were once at odds with one another, but now he claims they are "like this" as he crosses his fingers. He presses on, trying too hard as usual, and tries to get Kira to call him Julian instead of Bashir. However, when he attempts to hit on her, she tells him to stick with Dax. This finally silences the doctor.
As their runabout drops out of warp, the warp field does not collapse properly and they are engulfed in a white flash upon entering the wormhole. When they exit the Bajoran wormhole in the Alpha Quadrant, they are shocked to see the station is gone, instead orbiting Bajor much as it did during the occupation. Before either of them can react, the runabout's sensors detect a Klingon Vor'cha class attack cruiser moving towards them. Two Klingon officers beam aboard the runabout and are shocked to see Kira. Apologizing profusely, they offer to escort her back to the station; she simply nods, obviously confused.
Upon arriving at Terok Nor, the two Klingons confer with a Cardassian officer named Garak. Bashir and Kira board the station, where they are confused to see Garak and even more confused to see Kira Nerys.
Bashir politely asks where they are and Garak informs him that they are aboard Terok Nor, the center of authority in the Bajoran sector for something simply referred to as the Alliance. Kira observes that she and Bashir took a wrong turn at the wormhole, suggesting they return to their runabout. However, the other Kira, whom the Klingons and Garak refer to as the Intendant, seems to have other plans. Bashir attempts to intervene, only to be chastised as a "Terran" for his tone of voice. The Intendant believes she has an idea of who their visitors are, and if she is right, she tells Kira she cannot let them go. Dismissively, she orders one of the Klingons to put Bashir to work.
Garak and the remaining Klingon escort Kira as they follow the Intendant out the airlock area and onto an identical version of the Promenade. Large flags display what appears to be a winged version of the Cardassian emblem enveloping the Klingon emblem, and below the flags, exhausted Humans carry large pieces of machinery in service to the Klingons and Cardassians. A Klingon officer named Telok informs the Intendant that a Terran has been discovered attempting to stow away aboard a freighter and brings the man to her. Approaching the Terran, the Intendant takes on a compassionate tone, asking his designation; she is dismayed to hear he is a Theta and observes how long he worked to earn this designation. Her tone changes to business as she tells Garak to send the Terran to the mines. Garak wants to execute the Terran to make an example of the man, but the Intendant claims Garak has made a career out of setting examples. He presses the issue, pointing out that two other Terrans have been caught trying to escape and asking that he be allowed to conduct an interrogation at least. While the Intendant permits this, she warns Garak not to kill his prisoner.
Elsewhere on the station, an ore-processing section identical to the one on DS9 houses dozens of Humans, who perform the same slave-like role as their Bajoran counterparts once did in the "normal" universe. As Bashir is escorted to the processing area, Miles O'Brien warns Odo that they need to upgrade one of the machines' thorium containment cells or there will be an accident. The Klingon escorting Bashir brings him to Odo and informs Odo that Bashir does not know the rules. Odo asks Bashir for a designation and Bashir can only think of his name, which Odo interprets as a joke, slapping him. Again, Odo asks for a designation, so Bashir informs Odo he does not have one; Odo corrects him, adding "sir" to the end of the statement. A rhetorical response garners another slap. Bashir becomes visibly agitated as they talk, but it is apparent that Odo takes perverse pleasure in provoking him. Upon hearing that Bashir is a doctor, Odo sarcastically reminds him to scrub before he operates. Bashir is put to work but notices that O'Brien has observed the exchange with great interest.
Leading Kira and the guard escorting her to Ops, the Intendant passes several Alliance emblems before entering the office normally occupied by Benjamin Sisko. She sits and urges Kira to do the same, dismissing the guard, her eyes feasting on Kira like an excited child on Christmas. The Intendant reveals to Kira that almost a century ago, a human named James Kirk accidentally traded places with his mirror universe Terran counterpart and drastically altered the course of history on this side.
At the time of the switch, the Terran Empire was barbaric but strong. While in the mirror universe, Kirk met a Vulcan named Spock and had what the Intendant calls a "profound influence" on him. Spock preached peaceful reforms after Kirk left, rising to commander in chief of the Empire in the process of doing so; however, once he had completed his reforms, the Empire was too weak to defend itself from the newly-formed Klingon-Cardassian Alliance. Kira wonders how Bajor fits into the picture. The Intendant explains that the planet had been occupied by the Terrans for decades when the Empire fell. Upon becoming free, it petitioned for entry into the Alliance and became "quite an influential member" in later years. Her story finished, the Intendant wonders if the other side is similar at all.
Unfortunately, Kira informs the Intendant that her Bajor has not been so fortunate. The Intendant is eager to hear about life in Kira's universe, but Kira insists that she cannot stay. However, the Intendant does not know how to send her back, nor could she if she wanted to do so. The Alliance upon seizing power declared that any visitors from other universes must be killed immediately to prevent future incursions after the first crossover, but unlike Garak, she says she does not like using violence. Kira knows exactly what she means and that she is looking for an excuse not to kill Kira.
Kira solicits the Intendants help, as she feels a leader like the Intendant could teach her what she needs to know to bring about a stronger Bajor in her universe. "My side once changed the course of your history," she says. "Well, maybe your side can change mine." While the idea appeals to the Intendant, she says she will still have to kill Bashir. When Kira asks her not to, she says letting him live is too dangerous and the Klingons and Cardassians would not allow it; however, Kira knows herself too well and points out that the Intendant does not give a damn what the Klingons or Cardassians think. "Oh!" the Intendant croons. "You know how to manipulate me!" She agrees to go along with Kira's idea and calls for a guard to find her some quarters.
The next day, Kira, who has essentially been given free reign, visits the ore processing center to find a now-filthy Bashir pushing a cart full of ore. Mirror Odo greets her at the door. Like his counterpart on the other side, he prides himself on his efficiency. He offers assistance if she needs him to explain anything, and when she mentions that she has worked in ore processing before, he laughs. When Kira mentions the name Kirk immediately, having read about the transporter accident at the academy. He plans to befriend the mirror O'Brien in the hope that this O'Brien knows as much about transporters as theirs does; meanwhile, Kira tries to find other help.
Quark's is no different in the mirror universe aside from the clientèle, with a mixed group of Bajorans and Cardassians standing around a dabo table as Kira enters. Quark has heard of the crossover and remarks that Kira is the spitting image of the Intendant. However, he is surprised to find that Kira knows him. She claims that the two of them are close friends on her side and that her Quark does her a lot of favors. As her Klingon escort still observes them from the doorway, Kira nonchalantly mentions that her Quark gets things done for her that no one else can and inquires about a transporter. The Ferengi is aware of how the first crossover occurred and agrees to help her if she can show him how to send other people across. Although Kira begins to talk about revolving doors, Garak enters followed by two Klingons and yells Quark's name angrily.
Greeting Garak amicably, Quark attempts to act as if nothing is wrong. However, Garak informs him that he is under arrest for helping Terrans escape from Terok Nor. Quark claims he is a coward who does not stick his neck out for anyone, but the Terran whom Garak interrogated has said otherwise. Knowing what is about to happen, Quark pulls out a phaser rifle and attempts to escape, only to be dragged away by the Klingons. "I shall miss him," Garak observes. "He always let me win at dabo." Shortly thereafter, Benjamin Sisko and a group of Terrans enter, helping themselves to free drinks in Quark's absence, and Kira sees another potential window of opportunity.
Meanwhile, the exhausted Terrans are allowed a lunch break and Bashir seizes the opportunity to introduce himself to the mirror O'Brien. Handing what little food he has been given to one of the other workers, he makes his way over to where O'Brien is fixing a panel of some sort. Hearing that the two of them are best friends in the other universe piques O'Brien's interest and he wonders what he does on the other side. Bashir informs him that he is chief of operations of the station, giving him reason to pause his work and consider the possibilities. When Bashir describes the other details of his O'Brien's life, mirror O'Brien says his other half must have gotten the lucky draw.
Bashir switches subjects, asking how much O'Brien knows about transporters. While he is no expert, he claims he knows as much as any Terran. "I hope that will be enough," Bashir remarks, explaining about the transporter plan. O'Brien finds the plan untenable and believes Bashir is lying to solicit his help. While Bashir insists that he is sincere, the spell that came over O'Brien when he heard of his other half seems broken, as he goes back to work and tells Bashir he does not know him. Odo interrupts to announce that break time is over and Sisko has requested O'Brien's presence. O'Brien insists that he must finish his repair work, but as usual, no one listens to him.
Back in Quark's, Sisko and the other Terrans are enjoying themselves at the bar and he remarks that the Intendant called him all the way from the Fowla system just to see Kira. She observes that he and his friends do not act like typical Terrans. As he explains, the Intendant provides him with a ship in exchange for "duties" he collects from other vessels. While most Terrans are enslaved, he and his crew are allowed relative freedom because he amuses the Intendant. He observes that Kira must amuse her as well.
O'Brien enters the bar to ask what Sisko wanted, and seeing him seems to brighten Sisko's day. Referring to O'Brien as "Smiley" despite O'Brien's objection to the name, Sisko asks how he is being treated in an attempt to make smalltalk. He observes that Smiley does not like him, which O'Brien reluctantly confirms, evoking a laugh from Sisko. The fact that Smiley is not afraid to show his dislike is why he amuses Sisko. Getting to the point, Sisko tells O'Brien that his impulse driver coil needs repairs. O'Brien notes the problems in ore processing which he needs to fix first, but Sisko cannot be bothered with such things and orders him to fix the ship first. As the Intendant calls for Sisko and he leaves the bar, Kira realizes that she may not have any hope at all.
Kira enters the Intendant's quarters to find the Intendant in a bath tub with several Vulcan servants attending to her as Sisko sits on a couch facing the door. The Intendant wants to know if there is another Sisko on the other side, and on hearing there is, the idea of two of Sisko pleases her. As she speaks, Sisko gets up to check on his ship, obviously not amused, but the Intendant stops him to ask if she has hurt his feelings. Obediently, he replies, "I never had any to hurt," and exits.
Once Sisko is gone, the Intendant talks to Kira as the Vulcans help her out of the tub and dress her. She mentions that she has heard Kira is looking for a transporter, and Kira reminds the Intendant that she is looking for a way back home. However, had Kira come to the Intendant with her request, she would know that transporters were re-designed after the first crossover to prevent future accidents. That leaves the Intendant to wonder why Kira did not do so. As she approaches Kira, her voice betrays a combination of hurt and distrust. Kira reluctantly admits that she is afraid of the Intendant. "I don't want your fear," the Intendant confides as she stands face-to-face with Kira, "I want your love. If you can't love me, who can?"
The door chime rings and Telok informs the Intendant that Garak has arrived with a prisoner. She tells them to come inside and they drag Quark, who has visibly been beaten, with them. As Quark apologizes for what he has done, the Intendant kneels beside the Ferengi and comforts him, explaining that he helped the Terrans because he felt sorry for them. However, she reminds him that the Alliance needs the labor to process ore, for without the Terrans, nobody would perform such tasks. Rising to her feet, she tells Garak to give Quark a quick death and seems to all but forget about the incident as Quark is dragged away begging for mercy. Kira is aghast, but the Intendant, now in a happy mood, announces she plans to throw a party. "What shall we wear?" she asks her pet.
Kira enters her quarters carrying a lavender dress to find Garak waiting for her. "Lovely," says the Cardassian of the garment. "I do admire a well-tailored gown." He proceeds to explain that the Intendant will never let Kira go as she is clearly enamored with Kira. Describing how the Intendant talks about Kira constantly, Garak compares Kira to a Drathan puppy lig left on the Intendant's doorstep and hints at his true intentions as he makes a point of mentioning that the Intendant trusts Kira with her life. Kira points at the guard outside her door as evidence of how much the Intendant trusts her, but Garak arranged the guard, not the Intendant. "Oh, she trusts you, as much as she trusts anyone. So who better to betray her?" he suggests. Garak's plan is that the Intendant will be gone in the morning and Kira will take her place. Shortly thereafter, he explains that Kira will retire to Bajor and he will take her place, at which point he will become the Intendant and Kira and Bashir will be sent home. He leaves Kira to ponder the idea and adds that, should she refuse, he has arranged for Bashir rather than the Intendant to be gone.
Hurriedly entering the ore processing center, Kira warns Bashir that the two of them must escape tonight. She does not have time to explain the web of lies and treachery, but she tells him to be careful because he might be in danger. Regardless of where they go from there, she insists that they must find a way to the runabout. She tells him that there will not be much warning if an opportunity presents itself so he should be prepared.
On the Promenade, Kira finds Sisko half asleep, his eyes closed, leaning against a pillar. She claims to have valuable information that she is willing to trade, and he finds amusement in the idea that Kira has already "gone into business for herself." When she tells him she wants her runabout or a way off the station, he laughs. "She'll have my head ... or something else," he says of the Intendant's reaction to such a plan. Kira dispenses with the negotiations and announces that Garak is planning to kill the Intendant. However, Garak has been doing so since he first arrived on the station. She reveals the plot in hope that it will convince him she is serious, but he laughs and observes that the plan is more creative than Garak normally gets. Frustrated, Kira wants to know why Sisko does not seem to care about the fact that he and his fellow Terrans are slaves; he counters by arguing that he has made the best of a bad life for himself. Disgusted, Kira accuses Sisko of being no less a victim than anyone else; as she leaves, her words seem to weigh heavily on his conscience.
Kira attends the Intendant's party in Quark's that night wearing the purple dress and Garak greets her charmingly. Telok brags to his fellow Klingons about his time in service to the House of Duras, commenting on the unpredictable nature of Lursa and B'Etor, when one of Sisko's crewmembers accidentally bumps into him. He punches the Terran dismissively, adding, "Stupid Terran pig!" The Terran pulls out a knife and rises to his feet but does so with restrained anger as he knows he is not an equal. At seeing the Terran is willing to challenge him, Telok nods approvingly, ready for a fight. However, when Sisko shakes his head, the Terran puts the knife away. "What's wrong, Terran?" Telok taunts. "Lost your nerve?" Telok spits in the Terran's face and the man almost loses control, but another look from Sisko prompts him to restrain himself. Visibly disgusted, Telok orders the Terran to get out of his sight, and as the man does so, Sisko takes his place threateningly. However, the room shifts its attention as the Intendant enters.
The guests cheer as the Intendant enters followed by her Vulcan servants and the musician asks what her pleasure is. She tells him to play something bright in a happy mood and joins the festivities as Kira observes her, deep in thought.
Meanwhile, Bashir sits exhausted in ore processing in front of a pile of rocks. Odo approaches him from behind and kicks him, noting that Bashir is not accustomed to the work load and has much to learn. "It's a shame this is going to be your last night on the job," he adds with a hint of sadistic pleasure. His taunting is interrupted when, just as O'Brien warned, the thorium containment field on one of the machines short circuits. The Terran workers scatter as Odo contacts engineering, and Bashir uses the opportunity to grab the phaser of one of the Bajoran deputies. Still facing the deputy, he begins to back out the doorway following the panicked workers. Odo spots Bashir and reaches for his own phaser, but Bashir shoots the Changeling, causing Odo to explode and splattering goo everywhere. Not taking the time to gawk, Bashir leaves immediately.
Telok and some other soldiers can be heard in the distance as Bashir runs through one of the corridors and enters a conduit. A pair of Klingons runs by, oblivious to his location. He crawls a short way before he finds O'Brien attending a panel on the wall. However, when he solicits O'Brien's help, O'Brien claims not to see him and goes about sealing the thorium leak. Bashir realizes it is futile and remarks that he thought O'Brien was a decent man, which O'Brien insists he is. O'Brien is worried that the Alliance will find and kill him if he helps Bashir, but Bashir points out that O'Brien, as well as ever other Terran, is already dead. He begins to enter another conduit, but O'Brien points out that the runabout pads are through another conduit, asking if there is room on the ship for him. The two of them emerge in another corridor only to find the Klingons have cut them off.
Interrupting the party, Telok brings O'Brien and Bashir and informs the Intendant of what has transpired; she immediately looks at Kira furiously. She declares that Odo's death is her fault for keeping Bashir alive in the first place and laments Odo's death. Garak and the others observe closely as she proclaims that Garak will use Bashir as his "example," and kill him slowly in public view for all Terrans to see. When Kira attempts to speak, the Intendant threatens to have Kira join him. She then turns her attention back to O'Brien. As he has been a perfect worker for years, she wonders what got into him, and he tells her that hearing about life on the other side and himself being chief of operations made him realize that, whatever the other side is like, there has to be something better than life as a Terran. "Not for you, Mister O'Brien," the Intendant informs him. "Oh, he's going to be taking you with him – just not exactly where you thought he would be taking you."
With a nod from the Intendant, Garak begins to lead Bashir and O'Brien out of Quark's, but taking Garak's gun from its holster, Sisko intervenes, inspired by O'Brien's words. The Intendant does not believe what she sees and asks Sisko if he has lost his mind. He quietly replies, "No, I didn't lose it. I just... changed it." By this time, Kira and his crew mates have taken the cue and are all armed. They slowly exit the bar before Sisko shoots the panel above the door, locking it shut. As he does so, the Intendant is near tears; for all the disparity between them, she had true feelings for Sisko.
Kira warns Sisko as he escorts her and Bashir to the runabout pad that the Intendant will track him down wherever he goes. Bashir suggests that he and his crew come with them, but Sisko assures them he can stay ahead of the law. "Maybe we'll stir up some things on this side," he adds with a grin. On hearing this, O'Brien changes his mind about leaving and joins Sisko's crew, as Sisko says he can always use a good tinkerer and putterer. Kira thanks Sisko before she and Bashir board the runabout.
Disengaging the docking clamps, Bashir and Kira take the runabout straight to impulse and depart Terok Nor as quickly as possible. As they head for the wormhole, Bashir reports that the runabout still has a plasma injector leak from the warp core, which Kira is counting on to return them home. They mimic the conditions of their original entry into the wormhole that brought them to the mirror universe, but a Klingon cruiser heads straight toward them, nearly destroying the runabout. However, as the Klingons on this side know nothing of the wormhole, Bashir and Kira are able to maneuver toward it and enter. They are inside the wormhole when one of the runabout's systems short circuits and there is another brilliant flash of light.
In Ops aboard Deep Space 9, Commander Benjamin Sisko emerges from his office and asks if the crew has found anything. Odo stands next to Dax as she reports that a search vessel picked up traces of the runabout's warp signature and indications of a plasma leak, but no ship. There is an alert from the computer and O'Brien announces it is them, although their deflector grid is damaged. Sisko tells Dax to hail the runabout and a filthy Bashir can be seen next to a formally-dressed Kira. With a mix of annoyance and concern, Sisko asks where they have been. "Through the looking glass," Kira responds.