When TNT cancelled Crusade during the production of its first season, J. Michael Straczynski had already written the script for "End of the Line". This episode would have been the final episode of Season One.
In the article, "It's the Journey", which I wrote while Crusade was still in production, I predicted, "Maybe they'll find a cure in the second season, but uncover an even greater danger to the Interstellar Alliance." In a recent interview with IGN FilmForce, Joe Straczynski confirmed his plans for Crusade. "Yeah, they would have found the cure around year two," he says. So, what is the nature of the even greater danger that the Excalibur would uncover? The answer lies in "End of the Line".
The set up for "End of the Line" begins in "The Path of Sorrows" when we see a flashback to the destruction of the Cerberus nine years earlier. It continues in "To the Ends of the Earth", the other unfilmed Straczynski script. In this story, Captain Gideon destroys a Shadow hybrid ship like the one that attacked the Cerberus, but he learns that there may be more of them. He also learns of a communications signal that may lead him to the ship's home.
I'll be getting into some spoiler material below. Unfortunately, Bookface.com closed in January 2001 so the script is no longer available.
Gideon discovers that the ship that destroyed the Cerberus came from a secret EarthForce base. We've known for a long time that the Earth has been dabbling in Shadow technology. They have recovered and experimented on artifacts. They've sent an expedition to Z'ha'dum. Clark had a secret alliance with Mr. Morden. Ivanova fought against several EarthForce cruisers modified with Shadow technology during the Earth Civil War. In the short story "Hidden Agendas", we learn that the new Warlock class destroyers incorporate some Shadow technology.
However, now we realize that Earth's work with Shadow technology is far more advanced than previously believed. The Cerberus was destroyed early in Babylon 5's first season (during "The Geometry of Shadows"), long before most humans had their first hint that the Shadows existed from the video of Warren Keffer's ship being destroyed. The research was obviously well under way even before President Santiago's assassination.
"End of the Line" reveals a widespread conspiracy in the EarthForce surrounding the use of technology that has been forbidden by the Interstellar Alliance. Major Lee mentions that the Earth Alliance maintains a half dozen secret research bases, but it isn't clear how many of them are researching Shadow technology. They have also managed to keep it secret through many years and at least three administrations. Finally, from the end of this story, it is obvious that they are willing to go to great lengths to keep Captain Gideon from revealing their secret.
In the IGN FilmForce interview, Joe Straczynski continues, "Suffice it to say that - through a series of incidents - the Excalibur crew would have been considered traitors and have to basically be on the run. Further, the cure that Earth would have believed to be the right one would not in fact work as they think it would have worked. Our guys would find out about this, and no one would have believed them. As things unravel, it's a larger conspiracy, so basically - after the second year - the show you think Crusade is would be a whole different show, with much more depth to it, more political, more controversial in some ways, and would deal with the impact of technology on society, would cast our characters as renegades and loners without port, and turn the whole series upside-down."
So, the cast of Crusade might have ended up like Captain Sheridan, renegades trying to save the Earth from itself. Crusade was clearly not intended to be a five-year search for a cure. It would have been a far more interesting story worthy of existing in the Babylon 5 universe....
...Reading this script makes me even angrier that TNT cancelled Crusade. With the excellent ratings that Babylon 5 has been getting on the Sci-Fi Channel, we can hold out hope for the slim chance that Crusade will be resurrected. Wouldn't it be wonderful to see "End of the Line" on television one day?