In 2372, she and her colleagues, Hanor Pren and her brother Bejal Otner, visited Deep Space 9 to conduct field tests on a technique to create artificial wormholes. Although initial results were promising, it was found that the wormholes were unstable.
While on the station, Lenara became acquainted with Jadzia Dax. Their former hosts, Torias Dax and Nilani Kahn, had been married, and they found their past feelings for each other re-emerging. After Lenara was nearly killed on the accident aboard the USS Defiant, Jadzia voiced her willingness to resume their previous relationship, despite the cost of reassociation. However, Lenara was unwilling to accept exile from Trill society, and the two parted company. (DS9: "Rejoined")
As part of the defensive effort in the Dominion War, Kahn developed a way to seal the Bajoran wormhole without damaging it or harming the beings living within, by using a phase-conjugate graviton beam. The technique was put into practice in 2373 in order to stop a Jem'Hadar fleet from invading the Alpha Quadrant, but the attempt was sabotaged by a Changeling infiltrator disguised as Julian Bashir. The sabotaged beam in fact rendered the wormhole even more stable and resistant to collapse. (DS9: "In Purgatory's Shadow")
"Seems a shame to disappoint them. Maybe we should do something."
"We could get into a screaming match and start throwing things at each other."
"Not bad. Or I suppose we could throw ourselves at each other, profess our undying love for each other and complete disregard for Trill society."
"Doctor Pren would probably have a heart attack."
- - Jadzia Dax and Lenara Kahn
"Well, Torias used to be insensitive at times. But you have to admit, Nilani did do her share of overreacting."
"That's because you were a pilot and it made me nervous. Made her nervous. Torias being a pilot made Nilani nervous. I've never had quite this much trouble sorting out my feelings from those of a past host."
"I know what you mean."
"Probably another good reason why we're not supposed to spend much time together. We'd probably just get lost in the past."
- - Lenara Kahn and Jadzia Dax
"They suit you. It's really good to see you again, Dax. That sounds so strange. I mean, I'm looking at a different face, hearing a different voice, but somehow it's still you."
"I know. Every time I start to think of you as just Lenara, you'll smile or laugh and suddenly it's you."
- - Lenara Kahn and Jadzia Dax
"I thought I'd, thought I'd gotten over you. It's been so long and so much has happened. And now I know I haven't."
"Shh. I've missed you. I've missed you so much."
- - Lenara Kahn and Jadzia Dax, prior to sharing a kiss
"Everyone is trying to look out for us. Protect us from ourselves. But in the end, all that matters is how we feel and what we do about it. Because either way, we're the ones who have to live with the consequences."
"That's the tricky part though, isn't it? Living with the consequences. When you're not with me, when you're not around, it's like a part of me is missing. I want to be with you more than anything, but I don't think that I can do this. Dax, I am not like you. I don't have a little Curzon inside me telling me to be impulsive, to ignore the rules, to give up everything I've worked for."
"Can you really walk away from me, from us? After all this time, we're together. Don't throw that away."
- - Jadzia Dax and Lenara Kahn
In the first draft script of "Rejoined", Lenara's surname was "Yor". The episode's final draft script for "Rejoined" stated the pronunciation of Lenara's first name as "le-NAR-ruh CON". She was described, in the same script, as being aged approximately in her mid-thirties. This would put Kahn's year of birth around 2337. 
Two of the costumes worn by Thompson were later sold off in the It's A Wrap! sale and auction on eBay. The first was a long-sleeved dress top and corresponding bottoms, that featured a multicolored metallic brocade, purple accents around the collar and a blue chiffon drape, while the second was a full-length, long-sleeved, silver-blue dress with a textured floral pattern. Both costumes were sold for $228.50 each. The silver-blue dress was later reused and worn by actress Ramona Case in a later episode.   
On preparing for her role in the episode, Thompson said in a 2003 interview "...the prep for it was to quickly try to understand what a Trill is and what type of backstory that they may have created that they didn't put down on paper for these two people. And then to work with Avery [Brooks], and he was really big on backstory, and just trying to give us a history. First time working on Star Trek where a director wanted me to come in prior to the first day you start shooting, so to get Terry [Farrell] and I together. I felt very safe with him." Of working with Terry Farrell, she further commented "She was great. She was just so easy and comforting, very focused with me. She had a great sense of humor and she worked really, really hard. This episode was very important to her. And I think she and Avery knew that. I'm not so sure about her history throughout the series but I know that a lot of her heart went into this episode too. And it was nice that Avery brought us in to meet each other. And I feel like I'm a pretty comfortable person and she certainly was, and Avery wanted us to have that contact. She was great to work with. I just loved it." (Star Trek: Deep Space Nine, Season 4 DVD Hidden File 04)
Terry Farrell commented, "The great thing about 'Rejoined' was that nobody had a problem with the fact that they were both women – the only problem was that they were married in previous lives. Making that episode was a wonderful and emotionally-charged experience and I was really pleased of the finished product." 
Reception to the kiss scene was controversial, as Ronald D. Moore recalled, "Some of the response was pretty angry. Some felt betrayed, didn't want to see this in their homes. An affiliate down south cut the kiss from their broadcast. I remember thinking, it's been a long time since Star Trek was banned in the South. Maybe it's time that we get banned again." Similarly, Rene Echevarria noted, "My mother was absolutely scandalized by the episode. Shocked and dismayed. She told me, 'I can't believe you did that. There should have been a parental guidance warning.' But it's exactly what I wanted to happen, to sneak it right into the living room." (Star Trek: Deep Space Nine Companion, p. 279)
The Trill taboo against re-association was something Michael Piller came up with early on in the series, later expanded by Ronald D. Moore. As Echevarria recalled, "The existence of the taboo meant we could do a tragic love story. But it was Ron who had this inspiration to make the ex another woman. We could tell the same story and the taboo about re-association would track with our own taboo about homosexuality. We could tell the story without ever talking about the fact they were two women. (Star Trek: Deep Space Nine Companion, p. 279)
The decision to make Kahn a woman went all the way up to Executive Producers Ira Steven Behr and Rick Berman, as well as the studio executives. "They questioned us closely about our intentions and why we were doing it, and how it would work in the story, and how far we were going to go," recalled Ronald D. Moore. "They saw that we were sincere, that it was a good story, that we could say something with the show, that it was what Star Trek stood for and that it would actually be something to be proud of. They went for it." (Star Trek: Deep Space Nine Companion, p. 280)
Lenara's experiment to create an artificial wormhole was a MacGuffin, "to get us through the tale and to explain why Lenara was coming to the station," Moore explained. "It had to be a science project so that Lenara and Jadzia would need to work together." (Star Trek: Deep Space Nine Companion, pp. 280-281)
In his review of "Rejoined", Star Trek author Keith R.A. DeCandido thought Susanna Thompson gave a "simply superb performance" going on to write, "The chemistry between [Jadzia and Lenara] is perfect, as every scene they have together just sparkles. Probably the best is their first, as they awkwardly circle each other at the reception, noticing everyone looking at them, and as soon as they start actually talking to each other, they instantly fall into a routine as if they’d known each other all their lives—which they haven’t, exactly, but the memory of such is strong in both of them." 
The character appears in all four issues of the Star Trek: Divided We Fall comic miniseries and is featured on the cover of issue #1, "Crossfire". In the miniseries, Lenara is kidnapped by Verad Kalon and Ezri Dax helps to rescue her.
The seventh host to the Kahn symbiont, namely Damar Kahn, appears in a mission of the video game Star Trek Online, set in 2409. This suggests that in this continuity, Lenara died some time after "Rejoined" but prior to that year.