Even before Star Trek: The Next Generation ended its run, the franchise received its next spinoff in Star Trek: Deep Space Nine. The show was the first to be developed without original creator Gene Roddenberry’s involvement and probably because of that, broke many of Roddenberry’s rules for the Star Trek universe.
One of the biggest rules that Roddenberry had was to minimize interpersonal conflict between the Starfleet crew as he believed that people would be more professional in the future. However, in the pilot episode of Deep Space Nine, the makers introduced the then-commander Benjamin Sisko as a man angry with his captain, Jean-Luc Picard.
Gene Roddenberry’s important rule for Starfleet was broken in Star Trek: Deep Space Nine

Gene Roddenberry is the mastermind behind the Star Trek franchise that everyone now loves. The former military man reportedly pitched the series as Wagon Train set in space, placing the sci-fi genre’s explorative and philosophical storylines above the action and blockbuster nature of the genre.
When he was tasked with developing a spinoff/sequel to the original series, Roddenberry reportedly had a few rules that the franchise had to follow to make it align with his vision of the future. One of those was reportedly the lack of interpersonal conflict between the crew members as he believed that humanity would be more professional in the future.

However, the pilot episode of Star Trek: Deep Space Nine went against this cardinal rule when it introduced the series protagonist Benjamin Sisko going through a personal tragedy due to his captain Jean-Luc Picard. The pilot ‘Emissary’ begins during the events of The Next Generation’s episode ‘The Best of Both Worlds’ and the Battle of Wolf 359.
As the Borg intensifies its attack, Sisko loses his wife Jennifer during the attack and he blames Sir Patrick Stewart’s Picard for the mishap. This puts him in direct conflict with not just a crew member but a captain of the Enterprise. The confrontation between the two later in the episode is also intense, establishing early on that Sisko will not be a typical Roddenberry protagonist.
Writers of Star Trek were reportedly tired of Gene Roddenberry’s rules

While it is admirable to see Gene Roddenberry have a specific creative vision, a TV series is usually not an auteur’s work. Many stakeholders become involved as multiple episodes need to be written, directed, and aired. Hence, to make sure the series did not go too far beyond his control, Roddenberry reportedly made a guide for the writers.
However, his rules were reportedly not all too freeing for the writers who came on board the series, especially in the spinoff shows where he was not involved as much. William Shatner, who played Captain Kirk in the original series, claimed that the writers were feeling claustrophobic while working with the noted showrunner.
Shatner said in an interview with The Hollywood Reporter that Roddenberry would not be too happy with the changes the series has seen after he passed away. He said,
I haven’t watched the other ‘Star Treks’ very much, but what I’ve seen with glimpses of ‘The Next Generation’ is yes, the difficulty in the beginning, between management, was all about Gene’s rules and obeying or not obeying those rules…The fights that went on, to my understanding, were big because the writers had their difficulties. ‘We need some more material.’ ‘We need to get out of here. It’s claustrophobic.’
With him not being involved in Star Trek: Deep Space Nine, the series explored a lot more conflicts and characteristics that did not match Roddenbery’s rules.
Star Trek: Deep Space Nine is available to stream on Paramount+.
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