Travelling by himself, Miles O'Brien takes a runabout through the Wormhole. He narrates a personal log in which he says that "they" do not want him to warn the Paradas, although he admits that he does not know who "they" are. He recalls the events leading up to this point, and as he describes them, he enters a flashback.
Miles had just returned from a meeting with a species known as the Paradas in which they discussed security measures for upcoming peace talks. He awoke to find Keiko and Molly dressed and eating breakfast, at 5:30 am. Keiko seemed somewhat suspicious and Molly did not want Miles to give her a kiss, but he thought little of it as Keiko left their quarters with Molly.
Upon reporting for duty, O'Brien discovered an officer had begun working on the security arrangements without him, apparently under orders from Sisko. He decided to pay Sisko a visit but thought better of it when he saw Sisko and Keiko having a private discussion on the Promenade. Later, Sisko told O'Brien to report for an annual physical, and when asked about his discussion with Keiko, claimed it was about Jake Sisko's grades. After an overly thorough examination by Bashir, O'Brien believed people's strange behavior that morning must have been because he had contracted some sort of disease; however, Bashir gave him a clean bill of health.
Things became stranger as the day went on. Jake asked O'Brien for help with a science project, but when O'Brien mentioned his grades, Jake said they were fine. Additionally, problems he had been assigned to fix seemed to have been intentionally designed to make him spend additional time repairing them. Even Kira acted suspicious toward him. He reviewed the other officers' logs, which confirmed that Sisko and the others were observing his movements, although to what end it was unclear. When Odo returned from a meeting with the Paradas, he offered to investigate the stituation, a bastion of friendship in a sea of suspicion.
In his log, O'Brien alludes to having made other preparations while he awaited a response from Odo. As he pondered the matter at Quark's, the Ferengi approached him from behind and declared, "The odds are against you, O'Brien!" Although Quark was only referring to O'Brien's scheduled racquetball game with Bashir, the chief asked to change the subject. Quark brought the Paradas up, intent on finding out about the potential customers. O'Brien told Quark to look elsewhere for such information and began to leave as Odo asked him to come to the security office.
After a brief discussion, a strange look from Odo gave O'Brien reason to suspect that the conspiracy had widened. He was about to leave Odo's office when Sisko and Kira entered with phasers followed by Dr. Bashir with a sedative. "Who the hell are you?" O'Brien exclaimed, to which Kira calmly responded, "We don't want to hurt you." O'Brien used one of his improvisations to stun the crew members and took out two security officers before fleeing the Promenade.
O'Brien attempted an emergency transport to the runabout Rio Grande, but the computer responded, "Unable to complete request. Please contact station commander for assistance." He discarded his comm badge in a corridor to make it harder for the crew to track him and set up a series of force fields. Using maintenance conduits and his intimate knowledge of the station, he made his way to the runabout and escaped. He contacted Admiral Rollman of Starbase 101 to warn her that the command crew of Deep Space Nine was under some form of alien influence, but she ordered him to return to the station and assured him he would not be harmed. That was when O'Brien set a course for the Wormhole.
Now en route to the Parada system in the Gamma Quadrant, O'Brien is being pursued by the Mekong. Unable to reach the system before the Mekong overtakes him, he travels toward one of Parada IV's moons and manages to outmaneuver the other runabout, which assumes another course. He follows the Mekong to Parada II and beams to the surface, where he finds Sisko and Kira with a pair of Paradan rebels. One of the Paradans shoots him, and when the door opens, Bashir is behind it along with O'Brien - the real O'Brien. It is revealed that the Paradan government abducted O'Brien and created a replicant (clone) designed to assassinate the rebels' delegation at the peace talks. The clone was so closely modeled on the real O'Brien, he was completely unaware that he was a clone - presumably the Paradans intended to activate him at a certain point in time.
Before he dies, the O'Brien clone says Keiko's name and grabs O'Brien's shoulder. "What about her?" the real O'Brien asks. "Tell her... I love..." the clone whispers as he dies.