Captain Sisko notifies Jadzia Dax that a group of Trill scientists will be arriving soon at Deep Space Nine, and will be using the Defiant to perform experiments on wormhole physics. He tells her that the head scientist is Lenara Kahn, and offers to grant her a leave of absence while the Trill scientists are aboard. Dax tells him she would prefer to stay, saying "I can handle it."
Dax joins the other senior officers to welcome the Trill team aboard the station. When she meets Dr. Kahn, the two are obviously very familiar. When Major Kira notices the interaction and asks Dax about it, she answers "I know her. She used to be my wife."
Later on, Dr. Bashir fills in Kira on the "rules" governing proper Trill behavior. Once its host dies and the symbiont moves on to another, the newly joined Trill is forbidden from interacting with the family and friends of the former host, including children and spouses. Jadzia Dax has no contact with the loved ones of the former hosts of Dax, her symbiont, even though they remain very dear to her. In one of her former lives she was a man named Torias Dax, and he was married to a woman named Nilani Kahn. Torias died young in an accident, leaving Nilani a widow. Now she is Jadzia Dax, and Kahn is within Lenara, a woman. Their reunion is emotionally intense.
Trill society imposes a strict penalty on joined individuals who form relationships with people from former lives. If Jadzia and Lenara were to become close, they could be exiled from Trill permanently and their symbionts forbidden from future joinings and allowed to die at the end of their hosts' natural lives. Jadzia Dax resolves to keep her relationship with her beloved ex-wife purely professional.
The Deep Space Nine staff holds a party for the Trill science team. After the toast, Kahn tries to initiate some small talk with Dax to break the tension between them. They immediately warm up to each other and seem to get along as well as they did in their former lives. As the party draws to a close, they glance at each other, and both realize that it is going to be hard to suppress their feelings.
Lenara Kahn's team boards the Defiant and prepares their experiment. They are attempting to create an artificial wormhole. If they are successful, it will be the first artificial wormhole in history. The Deep Space Nine science team, led by Dax, assists the Trills. As she and Kahn work they gossip about old memories, and they make arrangements to have dinner together, with Dr. Bashir along as a chaperone.
That night at dinner, Bashir is an obvious third wheel, the two former spouses so involved in each other they barely notice him. When he is called away on a medical emergency, he leaves the two alone, and Dax admits that she is enjoying Kahn's company very much. She takes her hand.
The first trial of the wormhole is successful. An artificial wormhole is created for the first time ever, making Lenara Kahn a historic name in astrophysics. Dax is obviously proud of her, and puts her arm around her. Bejal, one of the Trill scientists and Lenara's brother, pulls his sister aside later and scolds her. He sees how she and Dax have been getting along and treading a dangerous line. He does not want to see Lenara make a mistake. She reassures him that she and Dax are maintaining distance and he has nothing to worry about.
She does not seem certain of this herself, though. She rushes to Dax's quarters in distress and they are finally open with each other about what is happening. They have fallen back into the rhythm they had when they were married to each other and it is becoming harder to stay apart. Finally they kiss. Lenara forces herself to leave Jadzia's room before it goes any farther.
Later, Dax confides in Sisko that she knows she is in love with her former wife. He reminds her, needlessly, that if she were to get back together with Kahn, they would be exiled from their homeworld and the symbionts would be precluded from joining with other hosts when their current hosts die. That would be the end of both of their symbionts' lives, and for a Trill, that is unacceptable. He says that if it were him, he would want to know if it is all worth it and whether he can live with the consequences. He concludes by stating that he would support Jadzia no matter what her decision.
The next portion of the experiment gets underway. During formation of the wormhole it explodes and nearly destroys the Defiant. Kahn is severely injured and caught behind a wall of plasma fire. Dax desperately rigs up a force field that allows her to reach Kahn, and drags her to safety, at the risk of her own life. It is at this point that Dax realizes Lenara is worth it and that she can live with the consequences.
The experiment finished, the Trill science team prepares to disembark, and return to their own labs to rewrite the calculations that caused the failure. Dax pays a last visit to Lenara Kahn, who is recuperating from her injuries. She pleads with her former wife, asking her to stay on the station. Both know that this cannot happen, but Dax does not want to lose Kahn again. She leaves in tears, but still watches from afar as Lenara heads toward her transport. With one last look at the brokenhearted Jadzia Dax, Lenara Kahn leaves Deep Space Nine.