After the Drakh infect Earth with a plague, Captain Gideon is recalled home and given a new mission. Using the Interstellar Alliance's newest and most advanced ship, the Excalibur, he and his crew must search uncharted space for a cure for the plague within five years before it wipes out all life on Earth.
Galen reunites with an old friend when Excalibur comes to the aid of an Earthforce strip mining operation on the isolated agrarian world of Regula IV. Earth's efforts to obtain a mineral that may help in the search for a cure to the plague are hampered by a mysterious saboteur and the appearance of a gigantic golden dragon...
Galen takes control of the Excalibur to go in search of the mysterious 'Well of Forever', an ancient and hidden place within hyperspace where powerful energies intersect; though his motivations prove to be very personal.
The Excalibur is recalled to Mars to participate in a conference of Earth Alliance Doctors hoping to co-ordinate the search for a plague, however a doomsday cult called "Sacred Omega" plans to take matters into their own hands to ensure the arrival of Earth's judgement without interference.
On Babylon 5, CaptainsGideon and Lochley must try to negotiate a deal with the residents of Lorka VII, a world known to posses a wealth of ancient technology that could aid in the search for a cure to the plague.
The Excalibur visits dead and deserted world that was once home to a race that was wiped out by the same plague that infected Earth, yet the cities and building appear untouched by the passage of time. The mystery deepens when one of the survey team meets a grisly end.
The Excalibur is ordered to a secret rendezvous where a Warlock class destroyer drops off a mismatched pair passengers with instructions to take them to Earth where they must take on lifepod containing an infected individual; Doctor Stephen Franklin, who intends to gain a greater understanding of the plague. While en route, Gideon rescues a stricken Captain Elizabeth Lochley and her damaged Starfury.
A further seven other episodes were assigned, three of which made it to the script stage but were left unfilmed, while "Tried and True" and the "Sword trilogy" did not complete the scripting phase, and the remaining two episodes of the intended 22 episode order were left unassigned.
The Excalibur gives chase to the ship that looks like the one that destroyed Gideon's ship, the Cerberus, many years ago. This episode would have seen the Excalibur crew return to using their black uniforms.
The second part of the planned "sword trilogy" would have been a very contained story, mostly featuring Gideon and Matheson in a room, talking. Dureena would have still been missing and mention would be made of trying to find her.
The Excalibur finally tracks the hybrid's signal back to it's home base and uncovers some shocking secrets about Earthforce, the techno-mages and their connection to the Shadows. This episode would have been the season finale, ending with a cliffhanger leaving a question-mark of whether Gideon is alive or dead.
According to posts by J Michael Straczynski, which are archived on jmsnews.com, TNT broadcast the episodes out of the intended sequence. The order of the episodes was then revised when they were re-broadcasted on the Sci-Fi channel, the Sci-Fi channel actually contacted Straczynski and asked which order he would prefer the episodes were broadcast. A third order was formally endorsed by Straczynski as the "true" chronological sequence of events for the filmed episode, as it appeared in The Official Babylon 5 Chronology (published in the pages of The Official Babylon 5 Magazine in 1999-2000). This particular ordering supersedes Straczynski's own "preferred" sequence from a strictly chronological and causal standpoint. The original broadcast order as set by TNT was used for the DVD releases.
Original broadcast order
Revised broadcast order (Straczynski's Preferred order)