Odo and Sisko interrogate Quark, who has been caught preparing for some vole fighting with Morn. Quark protests his innocence, but Sisko orders their voles confiscated before returning to Ops. There, Miles approaches Sisko wearing civilian garb and suddenly pulls a phaser on him. He forces the commander into a teleporter, and they transport onto a Terran raider. When Sisko asks where they are, Miles announces that they're "through the looking glass."
The commander quickly deduces that they're in the dimension that Kira and Bashir visited last year. This version of Miles, who goes by Smiley, tells him that he'll send him back home after he performs one mission. The Resistance against the Klingon-Cardassian Alliance is at a crisis point. Sisko's wife Jennifer is still alive here and working on a trans-spectral sensor array for the Alliance. Captain Sisko of this dimension has recently died in battle, so only Commander Sisko can convince her to switch sides. Otherwise the Resistance will try to kill her.
Though reluctant to interfere in this dimension, Sisko cannot allow Jennifer to die here as well, so he accepts. Sisko arrives at a resistance cell hideout in the guise of Captain Sisko, where he meets the mirror versions of Bashir, Rom, Dax, and Tuvok. Though the rebels are suspicious of Sisko due to reports of his death, he wins over the crowd by bedding Dax, who was his mirror's lover. He then campaigns to rescue Jennifer rather than assassinate her, with Dax and Smiley's support. Bashir and Tuvok oppose him, but Sisko punches Bashir, and that settles that.
On Terok Nor, Kira lounges with some love slaves who look suspiciously like Sisko while stewing about his betrayal, his death, and the general state of the station. She summons Jennifer to discuss the sensor array and ensure her cooperation. Jennifer wants peace and was not on good terms with her husband before his death, so she is willing but unenthusiastic about the plan.
As Sisko and Smiley launch their rescue operation, Rom appears on Terok Nor ahead of them and informs Kira of the impending operation. Sisko and Smiley's raider is ambushed, and they're captured. Dragged before the intendant, Sisko tries to seduce her with Captain Sisko's devil-may-care swagger. Kira still plans on killing him for his betrayal, but she's more than happy to play with him first. As Sisko languishes in confinement, Jennifer visits him for a confrontation with her wayward husband, and Sisko explains that he's there to rescue her. Jennifer is reluctant to defect, but Sisko sends a signal to Smiley to set the real plan in motion.
In Ore Processing, Smiley fiddles with some circuits to contravene security, overpowers a guard, and stages a slave rebellion. Meanwhile, Sisko takes up two disruptors and asks whether Jennifer is in. Though still dubious, Jennifer throws caution to the wind and joins him. Both groups fight their way through the halls to the docking bay, where they find Rom's body pinned to the bulkhead. It turns out that the ever-suspicious Garak tortured the Ferengi into revealing the rebels' real plan, and he's brought a whole squad of guards to put it down. He and Kira try to talk the rebels into surrendering, but they flee back to Ore Processing instead.
The guards quickly catch up and surround the rebels. Kira orders that everyone except Jennifer be killed, but Sisko reveals that he has used his knowledge of his universe's Deep Space Nine to change its command codes and start its self-destruct sequence. He promises to give Kira the new codes once all his people have made their escape. Kira tries to call his bluff, but he's telling the truth. She reluctantly lets them all go.
Back in the Resistance hideout, Jennifer demands to know who Sisko really is, because he's certainly not her husband. Sisko admits that her husband is actually dead and tells her to ask Smiley about all the details. Before he departs for his home universe, she gives him a kiss on the cheek.
- Becoming the Mask: Despite his initial reservations, Sisko seems to enjoy impersonating his far less moral Mirror Universe counterpart. For example, he appears to have no problems having sex with both Mirror Kira and Mirror Dax, despite the fact that his relationship with both is completely Platonic in his universe, and that he's been their friend and colleague for years (or decades, if you count Dax's previous host).
- Bed Trick: Mirror Jadzia seduces Ben thinking he's Mirror Sisko, who has to go along with it to maintain his cover. He doesn't seem particularly broken up about it, though. Apparently the reluctance he showed to her advances in "Fascination" only goes so far.
- Bizarre Alien Biology: Quark says that confiscating Morn's voles will "break his hearts."
- Captured on Purpose: Sisko arranges such a plan to get him and O'Brien onto Terok Nor so he can meet Jennifer and then escape the station with her.
- Continuity Cameo: Tuvok makes a brief appearance as a member of the rebellion and gets a few lines.
- Continuity Nod:
- Contrived Coincidence: There's no in-universe explanation why Mirror Dax and Mirror Bashir just happen to be among Mirror Sisko's crew. They seem to be there just so Terry Farrell and Alexander Siddig would have something to do in the episode.
- Death Notification: Mirror Kira telling Mirror Jennifer that her husband was killed. She's not terribly broken up.
- Depraved Bisexual: The obvious attraction Intendant Kira showed toward Major Kira in "Crossover" starts getting exaggerated into indiscriminate sexual voracity, a trend that continues through her appearances in later Mirror Universe episodes. Nana Visitor was reportedly not happy, as she'd intended the Intendant's vamping on the Major to be a sign of extreme narcissism, not a normal expression of her sexuality.
- Double Reverse Quadruple Agent: Rom is a member of the Resistance, but then it turns out he's a double-agent for the Alliance, but then it turns out he's a triple-agent for the Resistance.
- Evil Is Hammy:
Mirror Garak: PURSUUUUUUUUUUUUUUUUUUUUUUUUUUUE!!!
- Nana Visitor and Andrew Robinson are particularly over-the-top in this episode.
- Avery Brooks also breaks out the ham when impersonating Sisko's mirror counterpart.
- Guns Akimbo: Sisko during the escape.
- Has a Type: Kira was coocoo for Captain Sisko before he betrayed her and died. Now she lounges around with a black, human love slave. At least she knows what she likes!
- Impersonating the Evil Twin:
- Inverted by Smiley, who impersonates the prime universe O'Brien to abduct Sisko.
- The Mirror Sisko isn't exactly "evil", but he's certainly more of a bastard than the regular Sisko is. Jennifer notices the difference and eventually figures out that this Sisko is not her husband.
- Indy Ploy: When Sisko and Jennifer get into a firefight in a corridor:Jennifer: Now what?
Sisko: Uh, I'll think of something.
- It's a Long Story: Sisko, when Jennifer asks him who he really is.
- Literary Allusion Title: The name of this Mirror Universe episode is "Though the Looking Glass." This is of course a reference to Through the Looking-Glass, in which Alice steps through a mirror into another world. For bonus points, both this episode and the book that provides its title are second installments about return visits.
- Mandatory Line: The Mirror versions of Odo and Quark were killed in the previous Mirror Universe episode, so Armin Shimerman and René Auberjonois aren't seen once the story moves to the MU. Quark and Odo only appear briefly before the opening credits, discussing a mundane matter that has nothing to do with the rest of the episode.
- The Mole: Rom informs on Sisko's "survival" to the Alliance and informs them of how to capture him, but he's actually doing so as part of a plan to get Sisko and O'Brien aboard Terok Nor. Unfortunately, Garak finds out the truth eventually.
- Oh, Crap!: Mirror Kira, when she learns that Sisko changed the access codes to keep her from stopping the Self-Destruct Mechanism.
- Recruitment by Rescue: The whole idea—rescue Jennifer from Terok Nor so she can help La Résistance. (The alternative is to terminate her.)
- Self-Destruct Mechanism: Sisko activates it as part of his escape from Terok Nor.
- Series Continuity Error: Alliance ships are shown de-cloaking in this episode. A later episode ("The Emperor's New Cloak") uses a major plot point that the Mirror Universe doesn't have cloaking technology. This also contradicts the Enterprise episode "In A Mirror Darkly", where the NX-01 has a Suliban cloaking device. There are various Expanded Universe attempts to explain this apparent contradiction.
- Talk to the Fist: Sisko punches Mirror Bashir for mouthing off to him, on Mirror O'Brien's advice.
- Tap on the Head: It takes a single punch from Smiley to knock the Cardassian guard out cold.
- Title Drop: Mirror O'Brien provides it when he tells Sisko where they've beamed to."I guess you could say we just stepped through the looking glass."
- Took a Level in Jerkass: The circumstances of the previous Mirror Universe episode seem to have hardened Mirror Kira. Whereas before, she made a valiant attempt to limit bloodshed as much as possible, here she orders random executions and delights in telling Sisko's wife that he's dead.
- Wham Shot: Mirror Rom's dead body.