Odo has become worrisome at the number of new people arriving at the station due to the newly discovered Bajoran wormhole. While talking with Quark in his bar, Odo observes a man he recognizes and demands he leave the station. The man refuses and the two get into a fight that is broken up by Sisko. Odo explains to Sisko that the mane is Ibudan, a smuggler of goods to Bajorans during the Cardassian Occupation. Though considered a hero by some, Odo states that Ibudan let a young girl die when her parents could not afford the smuggled goods, and later killed a Cardassian officer, since gone free after the end of the Occupation. Sisko warns Odo that he cannot take action against Ibudan without any evidence of a crime being committed.
Later, Ibudan is found dead in one of Quark's holosuites. One of Ibudan's friends reports to Sisko and Kira that Ibudan was afraid Odo would kill him. No foreign DNA is found at the scene of Ibuban's murder, and the general populous of the station start to become suspicious of Odo, a shapeshifter without any DNA. However, Sisko does order a formal investigation and temporarily relieves Odo as head of security. Bashir discovers that Ibudan was performing medical experiments on a strange material in his quarters despite having no training as a doctor or scientist. Bashir continues to observe the samples in Sick Bay.
The crowds on the station become more hostile believing Odo as the murderer, and Odo is forced to hide in his office to avoid a mod forming outside despite Sisko's attempts to calm them down. Bashir suddenly arrives with new evidence: the sample from Ibudan has started growing into a clone of Ibudan. Sisko, Bashir and Odo determine that the murdered Ibudan was also another clone, set up to incriminate Odo. They discover the real Ibudan hiding on the station, and now with evidence, Odo is able to arrest him for the murder of his clone.
In a side plot, Miles O'Brien struggles to help his wife Keiko O'Brien get used to living on the station, as she is unable to follow her interests. Miles comes up with the idea of starting a classroom for Keiko to teach the resident children and others that come to the station, which Keiko is happy to pursue.