The episode is mostly set in the 25th century, starting in the year 2450. On a rainy night on Earth, the elderly Jake Sisko (Tony Todd) is visited by an aspiring novelist Melanie (Rachel Robinson), who is curious to learn why Jake gave up writing after publishing two successful books. Jake, knowing the time in his life is short, decides to tell her his story, revealed as flashbacks in the episode.
Many years earlier, when Jake was eighteen, he went with his father, Captain Benjamin Sisko, on the USS Defiant to observe the inversion of the Bajoran Wormhole, an event that only occurs every fifty years. The inversion causes a malfunction in the Defiant 's warp drive, but Sisko and his son are able to fix it. However, as they congratulate themselves, a bolt of energy discharges from the warp drive and strikes Sisko, causing him to vanish into subspace, a dimension in which he is frozen in time. Believing him to be dead, Jake and the rest of Deep Space Nine mourn for his loss, but a few months later, Jake catches sight of his father for a brief moment. A year after the incident, Captain Sisko appears again, remaining much longer than before, and Jake and the rest of the crew ascertain that his temporal signature is out of phase, but cannot correct it in the limited time. Before he disappears, Sisko tells Jake, "I need to know that you're going to be alright." He soon disappears again as Jake cries, "don't leave me!"
When the Klingon Empire assumes control of Deep Space Nine, Jake is forced to abandon his home of five years and give up any further hope of finding his father. Returning to Earth, he eventually decides to study writing, marry and settle down. Achieving success as an author, Jake is able to think less about the past. His father suddenly appears again, this time in Jake's home. Jake introduces him to his wife and shows him the books he's published. He apologizes to his father for abandoning his attempts to save him and instead moving on with his life. But Sisko is proud of his son's accomplishments and hopes one day Jake will give him grandchildren. When his father suddenly disappears again, Jake is traumatized and decides to help him by returning to school to study subspace mechanics, abandoning his writing career and marriage in the process.
Finally, fifty years later, the wormhole is to undergo another inversion. With the help of Dax, Dr. Bashir, and Nog (now a Captain in Starfleet), Jake attempts to recreate the events with the Defiant. The rescue seems to be going well when a malfunction occurs sending Jake into the white void of subspace with his father. During this brief "visit", Jake, who is now older than his own father, explains that he's brought the Defiant back to the wormhole to rescue him. Sisko is disappointed that Jake has abandoned his writing and marriage in order to save him. Realizing the rescue attempt is failing, he tells Jake to "let go", and begs him to promise he'll return to his true passions and live out his life for his own sake. Jake returns to normality without his father and tries to figure out what went wrong with the rescue attempt. But eventually he honors his father's request to rebuild his life by returning to writing.
On the night of Melanie's visit, Jake knows his father will appear again, and has injected himself with a lethal hypospray dose, believing that he is acting as a tether that is keeping his father frozen in time; by dying when Captain Sisko is present, Jake will allow his father to become unstuck and revert before the warp core incident. After seeing Melanie off, Jake waits for his father. Sisko appears as expected, and Jake explains everything to him, telling him that his death will give them both a "second chance", and reminds him to dodge the energy discharge. Jake dies in Sisko's arms; Sisko immediately finds himself back on the Defiant, and remembers elder Jake's advice, pushing himself and his son out of the way of the energy discharge, erasing the future timeline. As they return home together, Sisko gains a greater appreciation for his son, knowing he would have given up his life for his father, even though this future Jake would cease to exist due to his sacrifice of himself to save his father.
Melanie, the aspiring writer who listens to Jake's story, is played by Rachel Robinson, daughter of actor Andrew Robinson (who himself had a recurring role on the show, that of Elim Garak). Rachel Robinson also auditioned for the role of Ezri Dax.
Although most of the events depicted in the episode are erased when the timeline is reset, there are a few hints of what is to come: Jake does begin writing Anslem before the end of the season, and tension with the Klingons continues to worsen. And it is also possible that another hint would point to the Bajoran Prophets possibly having this middle-aged Jake from the future appear in present time to allow his father to fulfill prophecy later on through his own death, though this is not truly certain, however.