Crusade was designed as a five-year story arc like its parent series Babylon 5, though creator J. Michael Straczynski intended to resolve the Drakh plague storyline after just a season or two before moving on to other plots.

Conflicts between the producers and TNT executives led to the show's cancellation before the first episode even aired. Straczynski believed the network's interference was a deliberate attempt to get out of their contract by making him fail to deliver the series they claimed to want.

TNT's market research showed that Babylon 5's audience did not watch other TNT programming and vice versa, making a spin-off series unattractive to network management.

Only thirteen episodes were produced and broadcast, though at least four more had been scripted before production was cancelled.

The Sci-Fi Channel attempted to pick up the cancelled show to continue production but could not find room in its budget.

The true in-universe chronological order of episodes remains disputed, with at least four different orderings existing: the original TNT broadcast order, a revised order by Straczynski for Sci Fi Channel reruns, an official order published in The Official Babylon 5 Magazine, and a fourth continuity-based order inferred from dialogue.

Several completed but unfilmed scripts survived the cancellation, including 'To The Ends of the Earth,' 'Value Judgements,' and 'End of the Line,' which were published online on bookface.com in 2001, while other scripts like Peter Woodward's 'Little Bugs Have Lesser Bugs' were published later in 2011 as part of the Other Voices collections.

The complete series DVD set was released in 2004, almost five years after the show ended, and unlike Babylon 5's DVD releases, Crusade was kept in its original fullscreen format rather than being cropped and re-edited for widescreen.

The initial DVD release included a commentary by Straczynski, but he had it removed from later pressings after discovering that portions of it had been replaced with a different interview to conceal his harsh criticism of TNT.