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.
According to Babylon 5 canon, Gideon's Apocalypse Box is not the only one in existence. There are actually six, scattered around the galaxy.
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.
The cure to the Drakh plague was going to be discovered at the end of the second season. Whether it would have been used then has never been revealed.
The voice of the Apocalypse Box was actually Gary Cole's, distorted electronically to sound very ethereal.
The hated gray and red uniforms were going to be "accidentally" destroyed in a "laundry accident" in the second-to-last episode of the first season.
Patricia Tallman, who played Lyta in Babylon 5, was originally scripted to be in "Path of Sorrow" in a flashback with Lt. Matheson. But the deal fell through and they had to revise the script without her.
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 Babylon 5 (1993)). Koenig had already signed on to appear - and was reportedly very enthusiastic about the script - when the series was cancelled.
Although J. Michael Straczynski never revealed what the cure to the Drakh plague was, he did hint that it was of the "monkey paw" variety, i.e., the cure might actually be worse than the disease.
Part of Gary Cole's costume was a class ring for "Earthforce Academy". He kept the ring and wore it in his next role, as Lumberg in Office Space (1999).
The first eight episodes aired were actually the last filmed. The final five episodes with the "new" uniforms were the first filmed before TNT halted production to completely redesign the show's set and costumes.
Tracy Scoggins (Captain Elizabeth Lochley), Richard Biggs (Dr. Stephen Franklin), Maggie Egan (ISN Reporter Jane), John Vickery (Mr. Welles) and Jonathan Chapman (The Brakiri Ambassador) are the only actors to play the same character in both Babylon 5 (1993) and Crusade (1999).
At Wonder Con 2008, J. Michael Straczynski announced that Crusade is "finished", i.e. nothing more will be done with the series.
Although there were many theories, the origin of the Apocalypse Box was never revealed.