The adjustment period aboard Deep Space Nine continues as transplants from across the galaxy attempt to come to terms with their new life and each other. O'Brien's wife Keiko misses the U.S.S Enterprise and her career as a botanist. Sisko's son, Jake, plagued by loneliness, eases his boredom by befriending a rowdy Ferengi boy named Nog. Meanwhile, Odo is faced with a more pressing problem when he spies Ibudan, a Bajoran he once arrested for murder, gambling in Quark's. He attempts to rid the station of the criminal, first by ordering him to leave and later by asking Sisko to throw him off the station, but neither effort proves successful. However, Odo soon gets his wish despite this lack of cooperation when Ibudan is found stabbed to death in a Holosuite.
Sisko orders an investigation of the killing, only to find his son Jake is also in trouble for playing pranks around the station with Nog. Strangely, this awkward situation between father and son creates an opportunity for Keiko, who volunteers to supervise the children of Deep Space Nine by starting a school. Later, Odo becomes the prime suspect in the murder investigation when mounting evidence, including the fact that the killer was most likely a shape-shifter, points to him.
Deep Space Nine's residents soon become suspicious of Odo, and although many officers believe their colleague's claims of innocence, Sisko relieves him of duty as Chief of Security. Keiko also faces trouble in her own endeavors when members of the diverse space station community resist the idea of sending their children to a Federation school. While she tries to recruit students, Bashir works to prove Odo's innocence, experimenting with DNA fragments that were found in the dead Bajoran's Holosuite.
Discouraged by the public's response to her school, Keiko considers abandoning her plans but is encouraged to press on by her husband. Meanwhile, Odo finds himself ostracized by the public, as angry residents vandalize his office and threaten his well-being. Bashir continues his investigation of the DNA patterns found in Ibudan's Holosuite, hoping to solve the mystery by causing them to replicate into the form of the being it belongs to.
Responding to the tension aboard ship, Sisko and Kira order more security to protect Odo. As they confront an angry mob's demand for justice, Bashir provides a more definite solution to Odo's problem when he reveals the result of his experiment. The murdered man was not Ibudan, but a clone he created and killed in order to frame Odo for his murder. His rank restored, Odo soon finds the real Ibudan aboard his ship, and since murdering a clone is still a crime, he is finally able to arrest his man.