J. Michael Straczynski had completed the script for the season 1 finale before the series was cancelled, an episode titled "The End of the Line". The episode was to have Captain Gideon discover the origin of the hybrid-Shadow vessel encountered earlier in the series: a secret EarthForce project to combine human and Shadow technology. An EarthForce officer would have subsequently revealed that Techno-Mages were originally agents of the Shadows who rebelled, but still use the Shadows' technology. The friendship between Gideon and Galen would have been strained, not only by the revelation of the Techno-Mages' origins, but by Galen's admission that he was sent by the Techno-Mages to find any more leftover Shadow technology, and that was why he'd been helping Gideon in the first place. The episode, and the season, was to have ended with Gideon on Mars trying to expose the EarthForce experiments, only to be shot by an EarthForce sniper.
J. Michael Straczynski had completed the script for episode 14 before the series was cancelled, titled "To the Ends of the Earth". The episode would have seen Gideon using the Excalibur and the Apocalypse Box to hunt down the mysterious hybrid-Shadow vessel (the ship, as seen in flashback, that destroyed the EAS Cerberus), setting him at odds with other crew members. After a space battle with the Excalibur, the hybrid vessel would have self-destructed, and the final scenes of the episode would have suggested a connection between the hybrid vessel and EarthForce. The events of this episode would have set up the series' main story arc.
Crusade creator J. Michael Straczynski's recommended episode viewing order is as follows: Racing the Night, The Needs of Earth, The Memory of War, The Long Road, Visitors from Down the Street, The Well of Forever, Each Night I Dream of Home, Patterns of the Soul, The Path of Sorrows, Ruling from the Tomb, The Rules of the Game, War Zone, Appearances and Other Deceits. However, because of dialog looping during post-production and costume changes mid-season this viewing order will introduce minor continuity errors.
Fiona Avery had completed the script for episode 16 before the series was cancelled. The episode, titled "Value Judgements", would have seen the Excalibur crew encounter fugitive telepath Alfred Bester (Walter Koenig, reprising his role from Babilonia 5 (1993)). Koenig had already signed on to appear - and was reportedly very enthusiastic about the script - when the series was cancelled.
J. Michael Straczynski tried to remove his name from the writer credits. He registered the pseudonym "Eiben Scrood" with the WGA, but the WGA caved to pressure from Warner Bros. and would not allow the pseudonym.