Doctor Bashir finds Dax playing with an Altonian brain teaser, a puzzle responding to neural theta waves in a holosuite. Eager to get closer to her, he says he loves puzzles and volunteers to play. Before she transfers control to him, she casually mentions that she’s been trying to solve it for 140 years. As soon as she transfers control to him, the puzzle bursts in a matter of seconds. Dax tries to warn him about Trill relationships, but is saved by the appearance of Benjamin Sisko, picking her up for dinner. Unwilling to give up, Bashir gloomily tells the computer to re-start the puzzle after Sisko and Dax leave.
In Quark’s, Odo is sitting at the bar, keeping an eye on Quark‘s business. Both of them notice Chief O’Brien arguing with his wife Keiko at a table on the upper level. Keiko is miserable aboard Deep Space 9; with no need for a botanist, she has nothing to do, and also has doubts about the station as a fit place to raise their daughter. Odo denies being able to understand why humanoids place so much emphasis on mating with other members of their species; he himself has never “coupled,” as he had decided that the aggravation of a relationship, worst of all the need to compromise, which idea he already hates, far outweighed its benefits.
Having dinner in the bar, Sisko and Dax are still adjusting to their new relationship. Sisko has trouble seeing the young woman in front of him as his old mentor and father-figure, Curzon, which was how he had always seen Dax. Dax reminds Sisko that sometimes, relationships between Trills and other species do not survive the change of a host. Sisko assures her it will not be that way with the two of them – it is just a little uncomfortable now.
Glancing around the bar, Odo tenses up when he notices a Bajoran man playing at the dabo table. Odo goes over to the table and informs the man that he is unwelcome on the station. A fight breaks out between the two and, after Commander Sisko forcibly separates them, Odo tells the man he has 26 hours to leave DS9.
Elsewhere on the Promenade, a bored Jake Sisko approaches Quark’s nephew, the only boy on the station of any species close to Jake’s age, and tries to make friends. The Ferengi is standoffish at first, but grudgingly shares his name, Nog. Jake smiles, seeing the beginnings of a friendship.
In Sisko’s office, Odo explains his actions: the man, whose name is Ibudan, had lived aboard the station during the Occupation, smuggling medical supplies and other black market goods to the planet. Some Bajorans considered him a hero, but Odo saw him as nothing but a ruthless profiteer – he had once allowed a young Bajoran girl to die, when her parents were unable to afford his asking price for the drug that would have saved her life. A few years before, Odo had arrested Ibudan for killing a Cardassian officer who wanted a bribe to look the other way, and he went to prison for murder. Now, the Provisional Government has granted him amnesty, since “killing a Cardassian isn’t considered much of a crime nowadays.”
Sisko agrees Ibudan is undesirable, but does not see what they can do when he has not recently broken any laws. Odo vows to get him off the station, one way or another, and goes on the record saying, “Commander, laws change depending on who’s making them. Cardassians one day, Federation the next. But justice is justice, and as long as I’m in charge of security…” Thereupon Sisko interrupts, “If you can’t work within the rules, I’ll find someone who can.” Sisko dismisses Odo with a curt nod of his head.
Jake and Nog play a practical joke on the Promenade, releasing some Garanian bolites that infect a dining couple that harmlessly turn alternately blue, green, and yellow for a short time. A security officer catches the boys before they can run and marches them to the security office, while Keiko looks on disapprovingly. She doesn’t believe that children should have the same freedom as they did on Starfleet ships like the USS Enterprise-D. She later mentioned to Miles that the station should have a school.
Sisko, Bashir, Odo, and Kira are in the deactivated holosuite, looking at Ibudan’s dead body on the floor. Odo reports that, according to the security logs, the holosuite’s door was locked, and only opened twice – the first to admit Ibudan, and the second time, presumably, to let his killer exit.
There is also no evidence of a transporter being used within the suite. Sisko orders Bashir to sweep the suite for DNA evidence to identify all persons who have been inside the suite. Sisko orders Kira to inform all docked ships that their departures will be delayed as the crime is investigated.
In Ops, Sisko and Kira receive Zayra, a Bajoran businessman from the Promenade, who confides that Ibudan talked to him shortly before his death, and confided fears that Odo was going to murder him. Kira quickly discounts the accusation, but Zayra remains suspicious.
Odo investigates Ibudan’s berth on the Bajoran freighter he arrived on. According to the ship’s manifest, he was alone, but booked a room with two bunk beds. The ship’s officer had assumed he simply wanted the extra room. Examining Ibudan’s computer terminal, Odo finds an appointment book, stating that Ibudan had a meeting with Odo scheduled for the time he was murdered.
Keiko talks to Sisko in his quarters, with Jake present. She lobbies to open a school aboard the station, as there are no fewer than twelve children of school-age there. Sisko is more than happy to provide her with an empty room and some computer equipment; the only question is how many other parents aboard the station will accept her as a teacher. After Keiko departs, Sisko starts to read Jake the riot act, warning him to stay away from Nog, but Jake ducks into his room.
Bashir reports that only five persons’ DNA traces can be found in the holosuite: Ibudan’s, and those of the four officers who were in there after he was murdered. Kira is baffled: Ibudan entered the room alone, and the door stayed locked until his killer exited – which is impossible. Odo grimly says that the only explanation is that the killer was a shapeshifter like himself, who could enter the room through the cracks in the door.
Odo says in Ops that if he is being framed, it is a very “neat package”; only a shapeshifter could have entered the holosuite in order to murder Ibudan, Ibudan’s calendar said he was going to meet with Odo at the time he was murdered, and since Odo would be expected to investigate the murder, traces of his DNA would be left at the crime scene, regardless of whether he entered it earlier (during the murder) or later. Kira asks him if he has an alibi, and Odo confesses that he has to regenerate every 18 hours, and was shapeless in a pail in the back of his office when the murder occurred, so the answer is no. He asks Kira to instruct Bashir to do a sweep of Ibudan’s quarters aboard the freighter.
Quark’s brother, Rom, is initially hostile towards the idea of enrolling Nog in a Federation-run school, saying that a traditional Ferengi education is designed to teach young Ferengi the cutthroat skills needed to thrive in commerce. Keiko does a clever sell job, convincing Rom that she can teach his son those virtues, and more: learning commerce from the perspective of other cultures, his son’s future customers, will be a huge advantage. Rom appears thoughtful, and Keiko leaves him to mull it over.
In another corner of the bar, Zayra and several other Bajorans are questioning Odo’s innocence; after all, he is the purest form of alien, and all they really know of him is that he worked on the station when the Cardassians occupied Bajor. Quark, overhearing, cuts in and defends Odo: no one knows (and loathes) Odo better than Quark does, and whatever else he is, Odo was not a collaborator and is no murderer.
An unidentified, cloaked and cowled Bajoran is listening to the conversation.
Nevertheless, Zayra returns to Ops with a group of Bajorans for support, to confront Sisko with their suspicions. To avoid the appearance of a conflict of interest, Sisko feels he has no choice but suspend Odo for now.
In the infirmary, Bashir reports to Odo that he has found the destroyed remains of a biological sample container in Ibudan’s quarters. It appears that Ibudan was conducting some kind of medical experiment, but Odo says that Ibudan was neither a scientist nor a doctor. Bashir finds a small biological sample in the remains of the container. When he puts it into a solution to culture it, its cells begin dividing rapidly.
Odo is summoned to Ops, where Sisko reluctantly informs him that he is relieving him of duty. He assures Odo that he does not believe the Bajorans’ suspicions of him, but Odo sardonically replies that, with all the evidence mounted against Odo, Sisko would be inhuman if a small part of him did not believe Odo might be guilty.
Odo returns to his office and finds it vandalized: his datapads are littered all over the floor, his monitors have been smashed, and the word “SHIFTER” spray-painted across the wall. As he starts to clear up, Quark happens by and offers to find out who did it. Chafing at the idea of asking the Ferengi for help, Odo declines. Then he asks Quark if he would be interested in Odo working for him, since it looks like Odo will be out of a job soon. Quark is briefly enthralled by the idea of having a shapeshifter to use in his various dealings, before he realizes Odo is joking with him.
As he leaves the office, Quark mentions that he has been making some inquiries about Ibudan’s stint at Kran-Tobol prison, but he seems not to have made any enemies (who might be suspects in his murder) as he had spent most of his time hanging around the Bajoran dissidents jailed by the Cardassians for various non-criminal acts.
In the Infirmary, Bashir and Dax show Sisko the sample from Ibudan’s container, which has been growing exponentially and is now a large, flesh-colored blob. Both Bashir and Dax are sure it is a vital clue, but cannot yet say what it is. Sisko invites Dax to lunch, and Bashir, mistakenly thinking he is being invited as well, accepts. To diffuse the awkward moment, Dax begs off, leaving Sisko and Bashir to go by themselves.
Over lunch, Bashir admits that he is attracted to Dax, but does not want to step on Sisko’s toes, since Sisko has known “her” far longer. Sisko explains to the doctor that in all the previous years he knew Dax, the Trill was his male mentor and friend, Curzon. Therefore, Sisko assures Bashir, he is not interested in Dax romantically and the young doctor is free to choose to pursue Dax in that manner. Sisko and Bashir then witness Odo rejected by the customers at Quark’s who refuse to drink with, or even be near, the former chief of security.
Miles is helping Keiko to set up her new schoolhouse, and has replicated an old-fashioned schoolhouse bell. Molly, from her father’s arms, says that she wishes she could attend her mother’s school, and Keiko wryly responds that she does too, at least that way she would know someone would show up. They are interrupted by the sound of an angry mob on their way to Odo’s office screaming that he is a murderer and a freak. O’Brien signals Ops to have them send security to assist Odo and requests Commander Sisko’s presence to handle the mob.
From afar, Bashir observes the mob outside Odo’s office, trapping him inside and yelling for his head. Turning back to the infirmary, Ibudan’s “blob” amazingly has grown much larger.
Sisko and security arrive to see the mob growing larger and more violent. While Kira secures the turbolifts, more armed security arrives.
Sisko plants himself in front of the door and defends the Constable, telling the Bajorans not to condemn a man just because he happens to be different from them. Zayra and others begin yelling about the evidence against Odo. Meanwhile, Bashir and Dax are frantically analyzing the blob, which has grown larger still like a man-sized humanoid. Bashir makes a realization and they appear to the mob, announcing that they have a breakthrough in the case: the murder victim was not Ibudan.
Bashir’s pronouncement stuns everyone there, including Odo, and they lead Sisko and Odo to the infirmary, while Kira and O’Brien tell the crowd to disperse.
The man who was murdered was Ibudan’s clone, whom Ibudan created himself, specifically to kill, then to frame Odo for the crime. (As Odo later finds out, one of the dissidents with whom Ibudan had associated in prison was a Bajoran geneticist who had been jailed for conducting cloning experiments.) Bashir and Dax have already checked the victim’s DNA and found the signature gene sequence degradation that identifies him as a clone. Bashir predicts that the second clone will gain consciousness in about two days and be a more-or-less exact copy of Ibudan, though (Odo adds) hopefully not psychologically.
Now Odo concentrates on finding Ibudan, who turns out to be masquerading as an elderly Bajoran man who arrived a short time ago on a ship. Odo captures him as he boards the ship for departure from the station, pulling off his mask and informing him that killing his own clone still makes him guilty of murder.
In her empty schoolroom, Keiko glumly checks the time. Sisko enters with Jake, and, to her surprise, Rom enters a few minutes later with Nog. Nog starts to take the desk next to Jake’s, but Rom tells him to sit on the other side of the room, not wanting him to have anything to do with “that Human boy”; apparently he and Sisko are of one mind on this subject. A short time later, two other Bajoran children are escorted in by their parents, and Keiko happily introduces herself, and begins her lesson plan, with a basic introduction to Bajoran history.