[6] He remained good friends with Michael Piller and wrote the season 4 episode "Qpid" as a freelance writer.

Piller persuaded him to join the new series Star Trek: Deep Space Nine as a supervising producer.

As showrunner, Behr reported to head executive producer and franchise chief Rick Berman.

As executive producer, Behr was largely responsible for the story arc of the show, from Bajoran politics to the Dominion War.

[7] Behr wrote or co-wrote some of the most important episodes in the Dominion arc, including "The Jem'Hadar", "The Search", "The Way of the Warrior", "Broken Link", "Apocalypse Rising", "In Purgatory's Shadow", "By Inferno's Light", "Call to Arms", "Sacrifice of Angels", "Tears of the Prophets" and the final episode, "What You Leave Behind".

Behr also had a significant role in the development of the Ferengi alien race during his work on Deep Space Nine.

Along with fellow Deep Space Nine producer Robert Hewitt Wolfe, Behr also co-wrote Legends of the Ferengi, a collection of short stories involving the Rules of Acquisition.

Behr served as writer and executive producer on the short lived series Bob Patterson (2001), which was created by and starred Jason Alexander.

[17] From 2014 to 2016, Behr served as writer and co-executive producer on Outlander, alongside fellow Deep Space Nine contributor Ronald D.