An ongoing series with as heavy a story arc as Babylon 5 almost guarantees that the final product will look different from what was originally envisioned. In addition to normal creative changes, the real life departures of actors can cause plot changes on the show. As mentioned above, Straczynski wrote "trap doors" for the various characters, which were plot points which would allow them to be written out of the show. Often in retrospect the "ghosts" of potential plotlines can be seen among the earlier episodes. Among the changes which occurred over the course of the show were:
-The earliest change was casting. Between the B5 tv movie and the first season most of the actors playing human characters left the show. Rather than recasting the characters, Straczynski opted to create new ones, often with very similar characteristics. Dr Benjamin Kyle was replaced by Stephen Franklin, Lyta Alexander was replaced by Talia Winters, Laurel Takashima, was replaced by Susan Ivanova. Among the plot points which would later be taken up by other characters was stim addiction. In the pilot movie there are several references to Dr Kyle working too hard and too long, what would eventually lead Dr Franklin to use stims.
-Perhaps most significant was the departure of Michael O'Hare and the replacement of Jeffrey Sinclair with John Sheridan. Originally Sinclair was supposed to last for the whole series and was meant to both lead the battle against the Shadows as well as becoming Valen. Straczynski decided that this was two much for one character, a feeling which meshed nicely with O'Hare's desire t depart the show, and the role of the Captain was recast. John Sheridan would go on to fight the shadows while Jeffrey Sinclair would become Valen. Vestiges of this unified plotline can be seen in the show: one is Catherine Sakai, Sinclair's on-again-off-again love interest who, at the end of season one was sent on a mission to the galactic rim. When Sheridan was introduced it was revealed that his wife had apparently died on a mission to the rim. If Sinclair had stayed on Sakai would have fulfilled the role ultimately played by Anna Sheridan. Similarly when Captain Sheridan ultimately "dies" he dematerializes into energy, an effect which would likely have led to his becoming Valen.
-Another altered plotline was that of the "traitor." Babylon 5 was always supposed to have a traitor among her crew who was loyal to sinister elements of EarthGov, rather than to the station. Originally this was supposed to be Laruel Takashima. When she left the show the plotline was transfered to Susan Ivanova. However, when the actress who played Talia Winters wanted to leave the show the plotline was used to write Talia out.
-In the episode BSquared the crew learns that the previous station, Babylon 4, has been moving through time. Originally it was explained that a mysterious figure known as "The One" was bringing Babylon 4 forward through time in order to serve as a base. During the episode the crew experiences flashes from their past and future. During one of these, Captain Sinclair sees Garibaldi, apparently fighting to the death against an unseen foe who is destroying Babylon 5. One of the final scenes reveals that "The One" is in fact Jeffrey Sinclair, although he appears quite a bit older. Eventually the mystery was explained in season three when Sinclair brought the station forward a few years in time, becoming artificially older in the process, before travelling back in time with it to the first shadow war. Originally, however, it seems clear that the station was being brought forward in time to serve as base after Babylon 5 was destroyed by the shadows. The Sinclair shown in the episode was from decades in the future near the end of his life when he would eventually become Valen.
-As originally conceived, Delenn was supposed to be an androgynous character, played by an actress but with her voice altered to sound masculine. Her transformation in season two would involve not only become more human but also becoming female. This idea was scrapped before filming began although Delenn's makeup became more human between the pilot movie and the series.
-Originally Straczynski intended for Londo to assassinate Cartagia. When he was writing Cartagia's death scene, however, he decided that it would be better for Vir to do it.
-At the end of season four Claudia Christian, who plays Ivanova, departed due to contractual disputes. She was written out of the show as having taken over a new class of starship. In her place a new character named Elizabeth Lochley was written in to take command of Babylon 5, and an important story arc for season five involved Lyta Alexander's romance with the leader of a doomed colony of telepaths on the station. If Ivanova had stayed on she would have assumed command of the station and been involved in a romance with the telepathic leader.
-In the plotline involving the human civil war the character of General Hague was always intended to lead the rebel forces against EarthGov. However when the time came for the plotline to mature the actor who played Hague was not available so his character was killed off camera.