While experimenting with a keyboard, the musically untrained Dax inexplicably plays a melody she seems to remember from somewhere, then suddenly develops a short temper toward her fellow crew members. She soon wanders onto the Promenade, where everyone mysteriously vanishes. A robed, masked figure stands above her, then a longer version of the melody begins to play. Dax is gripped with fear as the figure appears again, blocks her path, then removes the mask, only to reveal another. She then backs into Quark, at which point the Promenade is bustling with life again — and the masked figure is gone.

Concerned about the hallucination, Dax has Bashir examine her. He discovers that her levels of isoboramine, a neurotransmitter that mediates synaptic functions between Jadzia and the Dax symbiont, are dangerously low. Aboard the Defiant, Sisko and Bashir go with Dax to the Trill homeworld, where the Symbiosis Commission's Dr. Renhol administers a drug to bring up Dax's isoboramine levels. But Dax later has another hallucination in which two men from the Commission, dressed in uniforms dated about a hundred years earlier, attempt to capture her.

Dax meets with Timor, one of the Guardians, who are unjoined Trill dedicated to caring for symbionts. He says Jadzia is really experiencing memories from one of Dax's previous hosts. Later, the Defiant's computer identifies the mysterious music as a piece composed over 80 years before by a Trill named Joran Belar. When Dax is shown a picture of him, she suddenly experiences another hallucination in which the masked figure kills a Trill doctor and is revealed to be Joran. Dax then has a seizure and goes into neural shock.

Dr. Renhol says that if Dax's isoboramine levels don't improve in forty-eight hours, the Dax symbiont will have to be removed and Jadzia's life sacrificed. Desperate to save their friend, Sisko and Bashir turn to Timor, but he becomes nervous and evasive, leading them to believe he is hiding something. They access Joran's file, and find it has been purged. Sisko and Bashir then contact Joran's brother, Yolad, who says his sibling was killed after murdering the doctor who felt Joran was not suitable for being joined with a symbiont. Then, Yolad confides that he believes his brother actually was joined, despite claims in the official records to the contrary. Sisko and Bashir realize then that the symbiont was probably Dax.

Sisko and Bashir confront Dr. Renhol just as she is preparing to remove the Dax symbiont from Jadzia, then reveal that they have discovered the cover-up. Dax was once mistakenly joined with Joran, and this knowledge was blocked from Dax's memory — but now the memory block is deteriorating. They also know that Joran's experience contradicts claims that only one out of a thousand people is suitable for joining. In reality, almost half the population can be joined, a fact that would cause chaos as everyone fought to possess the few prized symbionts. When Sisko and Bashir threaten to reveal this secret, Dr. Renhol allows them to try and save Jadzia. They return to Timor, who has Dax enter the pool of symbionts, where the memories of Joran are safely re-integrated with her other memories. She emerges ready to deal with this painful, secret past — a whole new lifetime of thoughts.