When It Rains . . . ( episode ) Sisko and Kira aid Damar ' s rebellion against the Dominion ; Bashir discovers that Odo is infected with the disease that is threatening the Founders . ( Part 5 of 9 ) Summary . Teaser . Having just lost the Second Battle of Chin ' toka , Starfleet ' s Miles O ' Brien has determined that the only vessel immune to the Breen energy dampening weapon was the Klingon Bird - of - Prey . The chief engineer of the " Ki ' tang " had coincidentally adjusted the tritium intermix of the vessel ' s warp core to compensate for a containment problem before the battle . As a result , Martok has ordered every Klingon vessel to make the same adjustments to their reactors to protect them from the Breen . Unfortunately , this " fix " works on neither Federation nor Romulan ships . O ' Brien forwards his findings to both the Starfleet Corps of Engineers and the Romulan Ministry of Science for more in - depth analysis . General Martok and Captain Sisko plan to use the Klingon fleet as a diversion , to occupy the attention of the Dominion and the Breen . In the meantime , Starfleet will continue searching for an answer to the Breen weapon , while hoping the Cardassian uprising , led by Legate Damar , grows in strength , to further sap Dominion resources . To assist Damar in his new role as leader of an underground movement , Sisko and Admiral Ross agree to send Kira to his aid ; with her years of experience in ( ironically ) the Bajoran Resistance , she has a lot to teach Damar in how to wage a guerrilla campaign . Putting aside her personal feelings , she agrees , and will also bring along Garak , whose experience in the Obsidian Order promises to pay dividends , too . Act One . In the infirmary , Bashir convinces Odo to give him a sampling of his gelatinous state , as the doctor is working on a means of rapidly creating synthetic replacement organs for the war effort . On Bajor , Kai Winn feigns concern over the disappearance of Solbor , whom she recently murder ed . Dukat , his true identity revealed to the Kai , continues to encourage her on her path toward unleashing the Pah - wraith from the Fire Caves . As she continues reading the sacred Book of the Kosst Amojan , Dukat offers to help her , but she refuses , saying the book ' s words are for her eyes only . On the station , it is revealed that Martok will be inducted into the Klingon Order of Kahless , a great honor . Kira and Garak enter the room to inform Sisko that Garak has found Damar . However , Damar believes that having a Bajoran leading them would reduce morale as a constant reminder of the failed occupation . In order to give Kira ( a Bajoran ) some sense of " authority " over her Cardassian comrades ( and students ) , Sisko gives her a battlefield commission of Starfleet Commander ( the highest rank Sisko can confer on another , as a Captain ) . This allows her to speak on behalf of the Federation . Later , after Kira dons her new , Odo morphs his attire to more closely resemble how he appeared as the Terok Nor ' s security chief ( when DS9 was under Cardassian control ) . Garak then wonders if Bashir could surgically alter Kira ' s nose . But Kira is unwilling to go that far and the rebels are just going to have to put up with her presence . Garak responds that they will tolerate her to a certain degree , but he warns her that she , a Bajoran , should never trust the Cardassians she will be working with and training . Act Two . In conversations with his officers , Damar reveals that the revolt is not going well . The Cardassians are depleted in several key supplies , including food , as their food replicators have been destroyed . Damar indicates that Garak and Kira will bring them Federation replicators . His officers express that having Kira with them will be awkward , but Damar indicates that Kira has skills that they need . The crew of DS9 greet Klingon chancellor Gowron , visiting from Qo ' noS in order to induct Martok into the Order of Kahless . Gowron , who puts the past to rest with Worf , arrives with a barrel of bloodwine to be shared by old friends . Doctor Bashir is speaking with Chief O ' Brien about how Ezri seems to be avoiding him . He indicates that he has called her to his office under the ruse of going over her medical test results , but really wants to get a sense of her feelings . When Ezri arrives , Bashir gets the wrong idea that she and Worf are a romantically - involved couple . As she tries to explain that they are only friends and that she ' s actually in love with Julian , his attention is diverted to a disaster in his lab : he discovers that Odo is infected with the same virus killing the Changeling s of the Great Link . He contacts Odo , now under way to Damar , to notify him of his findings . Act Three . Bashir thinks Odo contracted the disease while linking to the Female Changeling . He will keep on trying to find a cure and he ' ll ask Starfleet to share Odo ' s medical records with him . In the middle of the night , Dukat sneaks into the Kai ' s study , unlocking the book , and reading its secret text . Suddenly , a beam of red energy ( resembling a Pah - wraith ) leaps from the pages of the book into Dukat ' s eyes , blinding him . After Gowron awards Martok the Star of Kahless , Gowron informs everyone that he ( Gowron ) would be immediately taking command of the war effort ; thus , a day of honor for Martok has become bittersweet , as he loses his command . Worf explains that Gowron sees Martok ' s military successes as a threat to his position as Chancellor . Gowron wants to be the Empire ' s savior alone . Martok insists that he has no desire to challenge Gowron for his position because he is a soldier , not a politician . He also recalls that while he earned his position as General , Gowron became Chancellor through plotting and scheming . Worf also remarks that Gowron is nowhere near as good in strategy as Martok is . In spite of this , Martok nevertheless retains his allegiance to the Empire , regardless of its current direction . Dr . Bashir is attempting to get Odo ' s medical records from Starfleet Medical to use as a point of comparison for his own records , however he is constantly been referred elsewhere and told he doesn ' t have clearance . Eventually he gets to speak to Commander Hilliard who is authorized to release the information . Hilliard asks Bashir some questions regarding Odo and his contact with the female founder , and still denies him clearance . Bashir attempts to argue , however Hilliard tells him that they can ' t risk him finding a cure in case it reaches the Founder before threatening to report Julian to Starfleet Security if he doesn ' t drop the matter . Later at the Replimat , Bashir tells O ' Brien how Starfleet has practically accused him of being in league with the Dominion just for wanting to help Odo . They decide to speak to Captain Sisko in the hopes he has the clearance to access the file . Damar welcomes Kira to the headquarters of the Cardassian Liberation Front . While he is genuinely grateful for Kira ' s assistance , Gul Rusot still harbors long - standing ill will toward her , and makes no secret of it . Act Four . Kira and Garak begin educating Damar ' s group in the art of resistance . The resistance group is to be split into different cells . Odo also points out a base called Adarak , which is weakly defended . Damar and the other rebels initially balk at this attack plan , as it is guarded by fellow Cardassians . Kira convinces him that those Cardassian s are merely collaborators , and if the Dominion realizes the rebels won ' t kill their own , they ' ll station Cardassians at every base . Luckily for Bashir , Sisko had the clearance to obtain the medical files he needed , noting that there is more data than he expected . However while looking through the data , he realizes that it is simply the results of the scans Dr . Mora took of Odo just after he discovered him ( Mora having shared this with Bashir ) instead of the data from his last check - up at Starfleet . It is clear this is no accident . . . Bashir was intentionally sent the wrong data in the hopes of throwing him off the trail for a cure . Knowing this isn ' t something Starfleet Medical would do , Julian and Miles begin to wonder if Section 31 is somehow involved in the cover - up , since they wouldn ' t have a problem with letting Odo die if it meant protecting the Federation . At some point O ' Brien mentions Ezri , and Bashir says that she ' s involved with Worf . O ' Brien states that Worf told him they were just friends and that Bashir must have misunderstood her . As Martok clears out his office on Deep Space 9 , he and Worf contemplate on Gowron ' s decision to take over command of the fleet and trying to humiliate Martok at the same time . Worf notes that Martok is very popular among other Klingons and is regarded as a savior , something Gowron won ' t tolerate as he wants to be the Empire ' s only savior . Martok bitterly notes that he isn ' t looking for power nor does he have any interest in politics . . . he is a warrior who has rose through the ranks and fought many hard battles while Gowron has limited combat experience and schemed his way to power . Regardless , Martok is still willing to serve his chancellor and help defeat the Dominion regardless of motives as he feels it is owed to those who have been lost during the war . Worf tells Martok of his pride to be a member of his house . Trying to provoke Kira , Rusot questions Odo about his past association with Cardassians on Terok Nor , insinuating that Odo was himself a collaborator . Kira jumps to Odo ' s defense , but the cooler heads of Garak and Odo prevail . . . for now . Odo , however , begins experiencing his first signs of the sickness , but keeps it a secret from everyone else , even Kira . Act Five . On Bajor , the Kai informs a blind Dukat that doctors can find nothing wrong with his eyes ; his condition is obviously a punishment from the Pah - wraiths , who took away his vision for reading the sacred texts . By now , the Kai has discerned Dukat ' s true loyalties , which don ' t lie with her , so she summons a deputy to escort Dukat out into the street , helpless ; she refers to it as a " lesson in humility for a blind beggar " . Screaming as he is brusquely shown the door , Dukat is told by the Kai to return when he has recovered his vision ( i . e . , when he has once again found favor with the Pah - wraiths ) . Now alone with the sacred book , the Kai devotes her full attention to studying it . Gowron astonishes Worf and Martok by suggesting an aggressive course of action against the Dominion , rather than just holding the line until the Federation and Romulan vessels are up to speed . Martok and Worf are incredulous , noting they can barely hold present battle lines . Citing the element of surprise , and citing the glory to be had as saviors of the Alpha Quadrant and despite Worf and Martok ' s insistence , Gowron declares that his risky strategy is not up for debate , and will commence forthwith . Meanwhile , in sickbay , Quark brings some coffee to a weary Bashir and O ' Brien , as his way of helping find a cure for Odo . They cannot even let Sisko know , as the Captain would be forced to report it to Starfleet , and their efforts would be further thrwarted . Bashir decides to do a simulation to try and work out exactly when Odo was infected , only to discover it occured almost three years ago on the date that he was ' examined ' by Starfleet Medical . The two officers are horrified by the realization that Odo wasn ' t infected by the female founder as they ' d assumed . . . instead Odo was infected " by " Starfleet , as a Section 31 plot of genocide against the Changeling race , including Odo . Since Section 31 created the virus they reason the organization must also have a cure , but know that getting a hold of it will be easier said than done . Memorable quotes . " " Doctor , get to the point . " " " " I need to borrow a cup of goo . " " " " Excuse me ? " " " " I ' ll give it back ! " " " " Well , gentlemen , it seems as if the Klingon fleet is the only thing that stands between us and the Dominion . " " " " What have we come to ? " " " " Remember your place , Dukat ! " " " " I thought my place was in your bed . " " " " So , Martok , how does it feel to be the most famous warrior in the Empire ? " " " " I am grateful for the opportunity to serve . " " " " And you ' ve served well , but you ' ve borne the burden of this war for a long time . " " " " I ' d do it gladly , and I ' ll keep on fighting until the victory is ours ! " " " " No , my friend . I can ' t ask you to carry this weight forever . It ' s time for me to take . . . a more active role in this war . As of today , I ' m assuming direct command of our forces . " " " " Chancellor , I . . . I don ' t understand . Are you . . . unsatisfied with the way I have performed my duties ? " " " " Would I have given you the Star of Kahless if I was not satisfied ? You should be happy . You ' re a warrior again . No more meetings , no more reports to file . You ' ll be out there , savoring the heat of battle . I envy you . I intend to see an end to this war and soon . The Dominion will rue the day they heard my name ! ! " " " " Adami , I ' m not the same man I was during the Occupation . The Pah - wraiths have changed me . " " " " But they can ' t change what you did . Do you really think I could let myself be touched by a man whose hands are stained with the blood of my people ? " " " " When we do release the Pah - wraiths from the Fire Caves , your hands will be stained as well . " " " " The Pah - wraiths will spare those they find worthy . The rest are of no consequence . " " " " I warned you ! The text of the Kosst Amojan is for my eyes alone ! " " " " Doctor Mora was kind enough to share his data with me . This looks like the scans " he " did when he first found Odo . " " " " Are you sure ? That ' s a lot of numbers there . " " " " I saw it with my own eyes , not seven years ago . " " " " Section 31 must have created the virus , infected Odo , and then used him as a carrier . " " " " So that when he linked with another Changeling , he ' d pass it on , and eventually the entire race would be infected . " " " " 31 isn ' t just trying to stop us from finding a cure . They ' re trying to cover up the fact that they set out to commit genocide . " " " " Well , if they gave Odo this disease , then they must have a cure . " " " " We have to find a way to get our hands on that cure . " " " " Before 31 gets their hands on us . " " Links and references . References . 2309 ; 2369 ; 2372 ; 2374 ; Adarak Prime ; advisor ; Alpha Quadrant ; AR - 558 ; Badlands ; Bajor ; Bajoran s ; Bajoran interceptor ; Bajoran Resistance ; barrel ; beggar ; blind ; bureaucrat ; blinking ; bloodwine ; Breen ; Bronok ; Cardassia ; Cardassian Liberation Front ; ; Chancellor ; chief engineer ; Chin ' toka ; classified ; coffee ; collaborator ; commander ; commission ; cooling unit ; demotion ; deputy ; ; Eminence ; energy - dampening weapon ; Federation ; Ferenginar ; Fire Caves ; garrison ; genetically enhanced ; genocide ; head of security ( aka security chief ) ; heart ; Holy Grail ; House of Martok ; hyper spanner ; Kahless ; Khitomer ; Kira family ; ; Klingon Bird - of - Prey ; Klingon Empire ; " Kosst Amojan " ; Kronos ; liver ; medical exam ; medical record s ; Mogh ; Mora Pol ; morphogenic enzyme ; morphogenic enzyme analysis ; morphogenic matrix ; morphogenic virus ; murder ; muscle ; Obsidian Order ; Occupation of Bajor ; Order of Kahless ; organ replacement ; Pah - wraith s ; plasma relay ; physiology ; Quark ' s ; replicator ; resonance scan ; ; Romulan Ministry of Science ; Rondac ; runabout ; Section 31 ; sigma 9 clearance ; Solbor ; soldier ; sortie ; Starbase 375 ; Star of Kahless ; Starfleet Corps of Engineers ; Starfleet Headquarters ; Starfleet Medical ; Starfleet Security ; supervisor ; synthetic organ ; tactician ; Terok Nor ; Tora Ziyal ; traitor ; tritium intermix ; warp core ; weapons depot Unreferenced material . Kro ' jek