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Taylor joined The Next Generation staff at the beginning of the fourth season as a supervising producer, co-writing the second episode to go into production, "Suddenly Human". After two years, Taylor became co-executive producer with Rick Berman and Michael Piller and served as executive producer/showrunner for the (final) seventh season of The Next Generation. During this time, she received credit on a number of episodes, including Wil Wheaton's final episode as a regular character, "Final Mission"; the episode that introduced the Cardassian race, which featured heavily in Star Trek: Deep Space Nine, "The Wounded"; and the first of a two-part episode featuring Spock, "Unification".
During the last year of The Next Generation, Taylor worked with Rick Berman and Michael Piller to develop the fourth Star Trek series, Star Trek: Voyager. When The Next Generation production ended, Taylor transferred to the Voyager production staff and served as executive producer with Rick Berman during the first four years. At the beginning of the third season, when Piller moved to a reduced creative consultant role, Taylor became head of the writing staff (showrunner) and stayed in that role until the end of the fourth season, when she retired and handed over control of the writing staff to Brannon Braga.
During her time on The Next Generation and Voyager, Taylor wrote three Star Trek novels for Pocket Books: a novelization of "Unification" that she wrote at the same time she was scripting its first part, and two Voyager novels that expanded on the background of the characters she had helped create for the series. In Pathways, for example, she uses a fix-up presentation to describe several characters' childhood and early adult experiences leading to joining the Voyager crew.