The Battle of Chin'Toka was a total disaster, but O'Brien notes that a single Klingon ship proved resistant to the Breen's power-dampening weapon. Other Klingon ships can mimic its engine calibration to also resist the weapon, but the alliance will need time to invent a solution for other types of ships. In the meantime, the whole alliance will rely on the Klingon fleet. Martok is ready to initiate a guerilla campaign to buy the alliance time, and he's about to be inducted into the Order of Kahless by Chancellor Gowron himself. When the Chancellor arrives, however, he announces that he's going to take personal command of the fleet. Martok is insulted but remains loyal to the Empire. Gowron decides upon a recklessly aggressive strategy against the Dominion, which alarms both Martok and Worf, but they have no choice but to obey their chancellor.

Bashir borrows some of Odo's "goo" to study it in hopes of inventing a new source of artificial replacement organs. In the process, he inadvertently discovers that Odo has been infected by the same morphogenic virus that is afflicting the Founders. After alerting Odo, he requests Odo's medical records from Starfleet to study the virus's effects and create a cure, but he finds that Odo's records have become highly classified, and Starfleet is profoundly unenthusiastic about the prospect of a cure. Bashir recruits Sisko for his security clearance to obtain the records, but the records he receives have been tampered with. The doctor realizes that Section 31 is likely sabotaging his efforts. With more research, Bashir discovers that Odo was infected with the virus three years ago during his check-up with Starfleet Medical, suggesting that the virus itself is a Section 31 invention. Bashir concludes that Section 31 must therefore possess the cure, but he'll have to play his cards very carefully to obtain it. To add further complications, Ezri has been struggling to let Bashir know about her feelings for him, but a series of misunderstandings muddles the issue.

Meanwhile, Damar's Cardassian resistance is going poorly and needs help, so Sisko recruits the highly reluctant Kira to train the rebels on guerilla warfare tactics under a Starfleet commission. Odo and Garak accompany her, and they all arrive at Damar's base with much-needed supplies. In spite of their mutual hostility, Damar and Kira work together to reorganize the resistance into independent cells. Odo identifies a prime target to strike, but Damar balks at attacking a target with Cardassian defenders. Kira tells him that they cannot afford to avoid killing Cardassian collaborators. Damar's right-hand man, Rusot, tries to provoke Kira by calling Odo a collaborator, but Garak and Odo manage to defuse the confrontation. Odo, however, has begun suffering the symptoms of the morphogenic virus and hides this fact.

On Bajor, Kai Winn has grown cold and disinterested toward [[Characters/StarTrekDeepSpaceNineGulDukat Dukat]] now that she knows his true identity. She refuses to share her insights into the ''Book of the Kosst Amojan'', saying that the Pah-wraith text is for her eyes alone. Resentful, Dukat sneaks into her study to read the text for himself, but the book fires a beam of energy into his eyes and blinds him. Winn immediately finds out and reiterates that the text is for her alone. Bajoran doctors can't find anything wrong with Dukat's eyes, so he remains blind. Seeing him as useless, Winn banishes him from her presence until he can get right with the Pah-wraiths and restore his vision.
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!Tropes in this episode:
* AbortedDeclarationOfLove: Ezri is just about to confess her feelings to Bashir when he discovers that Odo is infected with the Changeling virus.
* AssholeVictim: Kai Winn throws out a blinded Dukat to beg on the streets.
* BatmanGambit: Bashir and O'Brien realize this was Section 31's plan when they infected Odo during mid-Season Four. The rogue agency knew that sooner or later, the Constable would link with another Founder again and ''wanted'' that to happen. Odo would then unknowingly pass on the disease and that Founder would pass it on to another Founder and so on until the entire Great Link would eventually become infected. If anything, Odo succeeded even ''better'' than Section 31 could've ever hoped, because he managed to infect the ''entire'' Great Link at the source during "Broken Link".
* BlackSpeech: The Pah-wraiths' texts are only meant to be read by a Kai. When Dukat makes the foolish decision to try and read them himself, he gets blinded for his trouble.
* CallBack:
** Kira recalls Damar's murder of Ziyal when Sisko orders her to help Damar's resistance movement.
** Bashir initially assumes that Odo contracted the morphogenic virus from linking with the female changeling back in season 6.
* CloningBodyParts: Bashir hopes to study Odo's "goo" and use its insights to create new organ-cloning technology.
* DarkestHour: Only Klingon ships can defend against the Breen's dampening weapon, leaving the alliance at a severe disadvantage. Additionally, Damar's resistance has been suffering high casualties.
* DontAsk: Bashir says this when O'Brien asks him how his talk with Ezri went.
* EasilyForgiven: Gowron decides that this applies to Worf, now that he's part of the House of Martok.
--> '''Gowron:''' The son of Mogh.\\
'''Worf:''' Chancellor.\\
'''Gowron:''' ''(to Martok)'' They say you've made him part of your House.\\
'''Martok:''' It's true.\\
'''Gowron:''' ''({{beat}})'' Then what is past is past. If Martok considers you his brother, that's all I need to know!
* EnemyMine: Kira and Garak working with Damar's resistance is very much this. Lots of TeethClenchedTeamwork.
--> '''Rusot:''' I don't believe what I'm hearing. When we were stationed on Terok Nor, you used to spend hours telling me how much you despised [Kira].\\
'''Damar:''' I did hate her, but that's a luxury I can no longer afford, and neither can you.
* EvenEvilHasStandards: Kai Winn is still disgusted that she's working with Dukat.
* FieldPromotion: A variation--[[ColonelBadass Kira]] is given a Starfleet commission with the rank of [[CommandingCoolness Commander]] in the hopes that the Cardassians will be more comfortable working with Starfleet, rather than the Bajoran Militia. If Bajoran Militia ranks are based on real life Army ones, this is actually a step ''down'': an army Colonel being equivalent to a naval Captain.
* GloryHound: Gowron wants the renown for himself, so he relieves Martok and steps in to steal leadership.
* HitAndRunTactics:
** Martok makes plans for his ships to use these against the Dominion.
** Sisko sends Kira to teach Damar these tactics.
* HonorBeforeReason: Damar and his resistance movement initially refuse to take Cardassian lives in service to their goals. Kira quickly disabuses Damar of the notion, pointing out that the instant the Dominion realises that Damar won't kill his own people, they'll post Cardassians at every potential target. Damar sees the logic in Kira's argument, and, while by no means happy about it, agrees that they can't reject any target, even if it costs Cardassian lives.
* {{Irony}}: Kira, a former Bajoran terrorist who fought the Cardassians, goes to teach her enemies how to become terrorists. Properly {{Lampshaded}}, of course.
--> '''Kira:''' You want me to go behind enemy lines and teach a bunch of Cardassians how to be resistance fighters?\\
'''Sisko:''' I'm aware of the irony.
* JerkassHasAPoint: Rusot's not exactly wrong that Odo collaborated with the Cardassians during the occupation, even if neither Kira nor Odo see it that way.
* KickedUpstairs: Gowron pretends that he's doing Martok a favor by giving him a prestigious award and relieving him of command so he can enjoy combat without the tedious paperwork and logistics of command. Martok isn't convinced for a second and sees it as an insult.
* LoopholeAbuse: Kira's the most qualified person to instruct Damar's resistance on tactics, but Cardassians aren't likely to enjoy being lectured by a Bajoran. Sisko's solution is to give Kira a Starfleet commission, as that will effectively make her a Federation representative.
* MotiveMisidentification: Once Bashir and O'Brian deduce Section 31's involvement in Odo's falsified medical records, they conclude that the rogue agency's trying to stop Bashir from finding a cure. While that's certainly ''a'' motive, they realize by episode's end that ''the'' motive is actually to conceal the truth that it was the agency that created the virus and used Odo to infect the entire Great Link.
* MyCountryRightOrWrong: Worf and Martok quickly realize that Gowron has taken personal command of the fleet [[GloryHound so he can take the credit]] [[ItsAllAboutMe for himself]], and that his plan to go on the offensive without their allies' support will only result in disaster, but Martok insists that it's their duty to follow his orders, no matter what.
* ObstructiveBureaucrat:
** Gowron himself. Canny politician, crummy tactician.
** Bashir runs afoul of Starfleet admins who won't let Bashir have the information he needs to cure the changeling's disease, since they'd rather the Founders die off if possible. It turns out that even more nefarious plots are afoot.
* OhCrap:
** Ross' reaction to Sisko telling him that they'll have to do the PalmBloodletting at Martok's ceremony.
---> '''Sisko:''' We're next.\\
'''Ross:''' ''({{beat}})'' You're kidding.
** Bashir when he discovers that Odo is infected with the changeling disease.
* OneThingLedToAnother: Ezri trying to explain to Bashir that her time with Worf helped her realize her feelings for Bashir--who, naturally, jumps to the wrong conclusion before she can finish.
* PalmBloodletting: It ''is'' a Klingon ceremony. Sisko and Ross aren't particularly thrilled that it's going to happen to them too.
-->'''Ross''': It still stings.\\
'''Sisko''': That's what the bloodwine's for.
* SeriesContinuityError: The catalyst for Kira becoming Damar's military advisor is that he's a conventional Cardassian soldier with no real guerilla warfare experience. However, Damar ''has'' spent a good chunk of Seasons 4 and 5 as Dukat's XO while he was waging his own guerrilla war against the Klingon occupation of Cardassian territory. It could be explained that Damar may have experience using a single ship to hit-and-run other ships but has little knowledge about leading an entire rebel movement involving clandestine operations, intelligence gathering, and sabotage. Alternatively, it could be that as XO, Damar's duties were more relegated to running the ship rather than helping plan Dukat's campaign.
* SpannerInTheWorks:
** Damar's Rebellion is one for the Dominion. It's completely stalled their post-Chin'Toka momentum and forced them to redeploy forces trying to hunt Damar down and quell his rebellion.
*** Similarly, the Klingon vessel ''Ki'tang'' ends up being this for the Breen energy dampening weapon. Nobody on the Dominion side could've foreseen that a Bird of Prey's chance engineering modification just before the Second Battle of Chin'Toka would render it immune to the weapon (and that all Klingon ships would follow this modification to render them likewise immune).
** Gowron taking direct command of Martok's forces likewise ends up being one for the Federation Alliance's own post-Chin'Toka momentum. It completely upends all the planning Martok and Sisko had devised for buying time for Damar's Rebellion and to develop a countermeasure for the Breen weapon.
** A variation, if not outright subversion, with Odo, who was never supposed to become infected with the Morphogenic virus. After all, he was Section 31's Typhoid Mary; they ''needed'' him to remain healthy and to serve as a viral carrier who could infect the Great Link. Odo becoming infected was a result of circumstances Section 31 never could've anticipated (i.e. Odo forcefully being turned into a Solid by the Link, changed back, and then re-infected during the Dominion occupation of [=DS9=]). What makes it a variation, if not outright subversion, is that the Spanner didn't occur until ''after'' Odo had already fulfilled his unknowing role in Section 31's plan. It's really more of a Spanner in the Works for the [=DS9=] crew rather than Section 31.
* TakeAThirdOption: Kira wants to assist Damar with his rebellion, but Garak expresses concern that Kira as a Bajoran military officer may cause some friction with the Cardassian Rebellion. While Admiral Ross is forced to agree with Garak, Sisko comes up with a way to get around some of these issues by giving Kira a Starfleet commission, complete with Starfleet Uniform.
* TantrumThrowing: After her confrontation with Rusot, Kira vents her anger on some cargo containers.
* ThinkNothingOfIt: When Martok is honored for his heroism, he says that he's "grateful for the opportunity to serve." (Considering that Martok was blacklisted by Kor and had to work as a civilian laborer for the KDF before earning a [[FieldPromotion battlefield commission]], this is more truth than most examples of this trope.)
* TooDesperateToBePicky: Rusot isn't happy about receiving Federation aid, especially with that aid coming from a Bajoran, but Damar refuses to turn down help.
-->'''Damar:''' We're in no position to turn down help, no matter where it comes from.\\
'''Rusot:''' Taking help from the Federation is bad enough, but having to take it from that Bajoran terrorist.\\
'''Damar:''' Kira Nerys has certain skills she's willing to teach us. Skills we need if we're going to defeat the Dominion.
* WhamLine: Bashir drops the bombshell on Odo.
--> "The disease that's killing your people -- you're infected."
* WhamShot: Bashir's simulation at the end of the episode when he's trying to determine when Odo was originally infected with the virus. Bashir and O'Brien both assume it should originate around the time of early Season Six when Odo linked with the Female Changeling...and then it keeps going back further in the series timeline...
* WithUsOrAgainstUs: Kira manages to convince Damar of this. If they purposefully avoid areas defended by Cardassians in their attacks, then the Dominion will quickly put their people in every possible location. The only available tactic is to attack any viable target, regardless of who guards it. Any Cardassian who isn't helping them, who guards the bases and would shoot them, is a collaborator and an agent of the Dominion.
* YouDoNotWantToKnow: Bashir to O'Brien regarding what [[NoSuchAgency Section 31]] might do to them.
* YouFool: Winn says this to Dukat when he gets himself blinded while trying to read the text of the ''Kosst Amojan''.