Inquisition ( episode ) An officer from Starfleet Department of Internal Affairs arrives at the station and accuses Dr . Bashir of being a Dominion spy . Summary . Teaser . Doctor Bashir is preparing to attend a medical conference at Casperia Prime as Odo teases him about the fact that such conferences are always held at sunny beachside resorts . As they talk , Chief O ' Brien enters the Infirmary , having dislocated his shoulder kayaking in the holosuite yet again . Bashir fixes O ' Brien ' s arm but warns him not to go kayaking for a while . The next day , the computer awakens Bashir at 0700 hours . He is extremely tired to the point where he has the computer confirm the time . Dragging himself out of bed , he packs to leave the station and bids farewell to his beloved toy bear Kukalaka only to have Captain Sisko ' s voice come over the intercom , telling all senior officers to report to Ops . Heading there with the intention of going straight to his shuttle , Bashir finds that Deputy Director Sloan has arrived from Department of Internal Affairs with a contingent of officers from Starfleet Security and is discussing something grim with Sisko . When Sloan and Sisko emerge from the Captain ' s office , they announce that Internal Affairs believes that there has been a major security breach on DS9 and a member of the senior staff has been passing information to the Dominion . Sloan will conduct an investigation , but for now the senior staff are relieved of duty and confined to quarters and Bashir is dismayed to find Sloan has already cancelled his appearance at the medical conference . Act One . Now in his quarters , Bashir orders breakfast from the replicator , but finds it out of order . The door chime rings , and one of Sloan ' s officers informs Bashir that Sloan wants to ask him some questions . However , things do not seem right as she escorts him to the wardroom ; a pair of officers carrying phaser rifle s run past them in the corridor , but Bashir is told not to worry about it . Sloan comes across as surprisingly charming when he meets with Bashir , casually asking about Bashir ' s experiences with the Dominion . They go over Bashir ' s imprisonment and his work with a group of genetically enhanced Humans , among other things . Before long , Sloan dismisses Bashir and promises to get the doctor his breakfast , as the replicators were taken offline as a security precaution . Later , Bashir is finally served his breakfast but finds he has been served gagh which was apparently meant for Worf . Examing his quarters , Bashir begins to suspect that someone has been there since he left as Kukalaka is now on his side but had been stood upright that morning , and a PADD that Julian had packed but since removed is now back in the bag . He then receives a message from O ' Brien , who says Sloan grilled the chief for over two hours – and every question he asked was about Bashir , making it clear Sloan suspects him of being the traitor . Once the transmission cuts out , one of Sloan ' s deputies enters and escorts him back to the wardroom . Act Two . After arriving , Sloan asks if Doctor Bashir received his breakfast . Bashir , guessing that he was intentionally denied any food , answers " Yes " . Sloan immediately wants to clarify his notes since his last meeting . Immediately , Sloan ' s tone of voice has changed from a nice , easy going tone in the last meeting to one that is more stern . He questions Bashir about the fact he was isolated from the other prisoners while at Internment Camp 371 for a number of days , with Sloan claiming that General Martok believes Bashir was gone for seven days instead of the five that the doctor believes . He also questions the relative ease of his escape , how his runabout was left in orbit of the prison and their cell was filled with everything he needed to construct a transmitter to get himself beamed to it . In Sloan ' s version of events , the Dominion " broke " the doctor during his time in prison and allowed him to escape . The allegation is that Bashir was coerced into spying for the Dominion but his memories are repressed ; as such , even if Bashir is spying , he hypothetically would not know it . When Sloan realizes he will not get anywhere with an interrogation , he has the guards escort Bashir – " in irons " – across the Promenade for all to see . Act Three . Later , Sisko visits Bashir in his holding cell telling him that Odo has discovered that Sloan had a son in Starfleet who was killed when his ship was destroyed by a Jem ' Hadar patrol . Sloan then enters and admits that he believes Bashir supplied them the information that allowed the Dominion to target his son . When Sloan initally refuses to allow Sisko to talk to Bashir alone , Sisko uses his authority as commanding officer and demands to be allowed to see Bashir when he likes and to sit in on all interrogations to make sure his rights aren ' t breached . Sloan is forced to agree , and Sisko promises Bashir to get him out of this . In the next interrogation , Sloan brings up when Bashir worked with a group of Jem ' Hadar in an attempt to free them from their need of Ketracel - white . Sisko argues that his happened before Bashir allegedly became a Dominion spy , but Sloan asserts that this proves Julian was already sympathetic to them . He then brings up that , while working with the genetically - enhanced Humans , Bashir gave them access to classified information and then recommended that Starfleet surrender to the Dominion . Bashir insists that he was just trying to save lives , but Sloan doesn ' t accept this argument . Captain Sisko is forced to state he also didn ' t agree with the findings and admits that Julian has made some very poor judgement calls recently but argues that doesn ' t mean he ' s a traitor and that all the evidence Sloan has is circumstantial . Sloan then questions Sisko ' s loyalty towards his officer , reminding him that Bashir only came forward about his genetic enhancements because he was found out . Had he not been , Bashir admits that he doesn ' t know if he would ever have come forward with the truth . After the interrogation , Bashir apologizes to Sisko for not telling the truth about his genetic enhancements . Sisko decides to put that issue behind them , and tells Bashir that while he doesn ' t think he ' s lying asks him to consider the possibility he was broken in the Interment Camp , became a Dominion agent and repressed the memory . Bashir insists that , while such a procedure is a medical possibility , he is certain that it didn ' t happen . Captain Sisko tells Bashir to sleep and they ' ll talk later . In the night , Sloan visits Bashir to tell him he an order from Starfleet Command allowing him to " neutralize threats " to security , and he plans to put Bashir in a maximum - security prison until the war is over unless Julian is willing to sign a full confession . Bashir tells Sloan where he can stick the confession and is about to allow himself to be removed when he is suddenly transported off the station by a Dominion - style transporter beam . Bashir now finds himself aboard a Dominion warship , where Weyoun tries to convince him that he is in fact a Dominion spy . Act Four . According to the Vorta , Bashir has gone through the same debriefing process a number of times , and the fact that the doctor does not believe his story does not surprise him . But rather than believing himself to be a spy , Bashir comes to believe Sloan is in fact the traitor . His conversation with Weyoun is interrupted as the ship comes under attack and Bashir is beamed aboard the . This time , the crew all believe Bashir is a spy , and he is at a loss for words for why he was beamed aboard the Cardassian ship . His story about Sloan only sounds even more incredible . As Bashir turns to O ' Brien for support , the chief pushes him away , but Bashir realizes something is amiss . The chief ' s shoulder was dislocated previously , which leads Bashir to realize that none of the people around him are who they say they are . Suddenly , the " Defiant " s bridge disappears and Bashir finds himself in a holodeck aboard a Federation starship , surrounded by three men in black uniforms , one of whom is Sloan . Act Five . Sloan motions for one of his lackeys to remove an implant from behind Bashir ' s right ear but the doctor reacts defensively . Therefore , Sloan gives Bashir the honor of removing the implant . The recording from the implant show that without a doubt , Bashir has unquestionable loyalty to the Federation . Sloan also comments that had they known about O ' Brien ' s injury beforehand , then they would ' ve incorporated it into the program . Bashir then deduces that he was beamed off of DS9 in his sleep so that no one would notice his absence . This explains a number of things , among them why Bashir was so tired at the start of his day . Tired of games , Bashir demands to know who Sloan works for . Sloan reveals that he is part of a covert organization known as Section 31 , which he claims was part of the original Starfleet Charter but answers to no one . And they are charged with covertly dealing with threats to the Federation – by any means necessary . Bashir asks what would happen if he was actually proven to be a Dominion spy . Sloan answers that they wouldn ' t be having this conversation now . Bashir voices his disapproval of Section ' s autonomy and blatant disregard for the founding principles of the Federation . Sloan tries to recruit the doctor into the organization , citing how Bashir likes to play spy in Quark ' s holosuites and his genetic modifications that were overlooked to continue his medical career . Bashir tries refusing , threatening to expose Section 31 but Sloan isn ' t threatened and promises that Bashir will eventually come around his way of thinking . As a result , Section 31 agents sedate him . When he returns to DS9 , Bashir learns from Odo that he was abducted the same time he was to go to the medical conference . Kira reports to Sisko that there were no traceable transporter signatures in Bashir ' s quarters , meaning that Section 31 must ' ve gotten him off the station another way or may be in use of transporter technology that they cannot detect . Bashir asks Sisko if Starfleet has come up with anything . Sisko states that that there is no record of anyone called Director Sloan or Section 31 , but Sisko ' s investigation with Starfleet Headquarters on the matter turns up some odd results . Sisko receives neither confirmation nor denial of Section 31 ' s existence , only promises to look into the matter . However , they didn ' t say " when " they ' d report back , implying a conspiracy . Bashir comments his surprise that Starfleet would sanction this type of black ops activity . Odo points out that Section 31 is comparable to the Romulan s ' Tal ' Shiar or the Cardassian ' s Obsidian Order . Bashir refutes that point , asking if they would sacrifice their own principles . Sisko has no answer for that . Kira suggests that they try and track down Sloan themselves but Odo reminds everyone that if Section 31 has existed since the birth of the Federation , then they ' ve learned to cover their tracks effectively . Whatever the true nature of Section 31 may be , Sisko says they don ' t have to go looking for them : Section 31 will come to them . Next time they meet , Sisko wants Bashir to accept membership to bring the organization down from the inside . Odo muses that Bashir will finally be able to play spy , but this time for real . Memorable quotes . " " Hot buttered scones , moba jam and some red - leaf tea . . . . please . " " " " Ugh . It ' s a little early for gagh . Well I hope you ' re enjoying my scones , Worf . " " " " We ' ll get you out of this , Julian . " " " " I ' m sure it ' s all a mistake . " " ( Quark whispers to Kira ) " " Isn ' t it ? " " " " I won ' t deny that Doctor Bashir has made some . . . questionable decisions in his career , but that ' s a long way from convincing me he ' s a traitor . Now so far , your case is based on circumstantial evidence and speculation . " " " " What other kind of case can I make against a man who covers his tracks so well ? " " " " That ' s a circular argument and you know it ! " " " " Congratulations , Doctor , it ' s not often that we ' re proven wrong . " " " " I take it you finally believe I ' m not working for the Dominion . " " " " I ' m leaning heavily in that direction but to erase any lingering doubts , what do you say we make one final test ? " " " " I ' ve finished playing games with you , Sloan ! " " " " I can assure you , Doctor , this is no game . " " " " And what does Section 31 do – apart from kidnapping Starfleet officers ? " " " " We search out and identify potential dangers to the Federation . " " " " And once identified ? " " " " We deal with them . " " " " How ? " " " " Quietly . " " " " Isn ' t it ? Because if what you say to me is true , you function as judge , jury , and executioner , and I think that ' s too much power for anyone . " " " " I admit it takes exceptional people to do what we do – people who can sublimate their ambitions to the best interests of the Federation . People like you . " " " " No , I ' m sorry . But the ends don ' t always justify the means . " " " " How many lives do you suppose you ' ve saved in your medical career ? " " " " What has that got to do with anything ? " " " " Hundreds ? Thousands ? Do you suppose those people give a damn that you lied to get in Starfleet Medical ? I doubt it . We deal with threats to the Federation that jeopardize its very survival . If you knew how many lives " we ' ve " saved , I think you ' d agree that the ends " do " justify the means . I ' m not afraid of bending the rules every once in a while if the situation warrants it . And I don ' t think you are either . In time you will agree with me . " " " " I can ' t believe the Federation condones this kind of activity . " " " " Personally , I find it hard to believe they wouldn ' t . Every other great power has a unit like Section 31 . The Romulans have the Tal Shiar , the Cardassians had the Obsidian Order . . . " " " " But what does that say about us ? When push comes to shove , are we willing to sacrifice our principles in order to survive ? " " " " I wish I had an answer for you , Doctor . " " " " Well , congratulations , Doctor . Looks like you ' re going to get to play a spy after all . . . only this time , for real . " " Links and references . References . addiction ; Bandee ; barbarian ; bedside manner ; Bopak III ; Cardassian s ; Casperia Prime ; Changeling ; confined to quarters ; conflict of interest ; ; Department of Internal Affairs ; dislocation ; Dominion ; Dominion War ; engramatic dissociation ; executioner ; ; Federation ; Federation Council ; framing ; " gagh " ; handcuffs ; holosuite ; Internment Camp 371 ; interrogation ; Jem ' Hadar ; Joint dislocation ; judge ; jury ; kayaking ; Kukalaka ; Moba jam ; Martok ; Milky Way Galaxy ; neuro - synaptic relay ; Obsidian Order ; Promenade ; raktajino ; red leaf tea ; Risa ; Romulan s ; runabout ; scone ; Section 31 ; shoulder ; Special Order 66715 ; Seventh Fleet ; springball ; Starbase 53 ; Starfleet General Orders ; Starfleet Medical ; sunscreen ; Tal Shiar ; thumbprint ; tricorder ; Tyra system ; Vorta