OK, doing this in reverse order: I've already written the rest of this post (so my fingers are getting rather tired), and am now writing this, the lead paragraph. I have in my possession Babylon 5 Script Book #15, but I'm too exhausted to explain what that is for those who don't already know, so read this thread if you want to know:
http://www.trekbbs.com/showthread.php?t=50006
And here is a shameless plug for all of the B5 script books:
http://www.babylon5scripts.com/
The most talked about feature of Script Book #15 is JMS's 7 page, single spaced synopsis of “the original story arc”, with Sinclair in place during the whole story. It's a bit of a misnomer to call this the “original arc”, as there were in fact earlier iterations of the story, before it got to this point, but this is where things stood in JMS's head at the time Season 1 was going into production (but after “The Gathering” was filmed). He wrote the document as sort of a memo to himself, so he could keep the big picture straight. The arc was written out in much greater detail on over 100 3x5 notecards, and on an encrypted file he had on his computer. But this was his summary.
Somehow or other, I volunteered to write out a detailed synopsis of JMS's 7 page story outline, and post it here for your benefit. That's what this thread is. I haven't quoted any of the outline directly. Just explained it in my own words. AFAIK, my synopsizing of JMS's synopsis is not in violation of his wishes. But if anyone wants to argue for why I should edit / delete this post, I'll hear you out.
A few things about the synopsis:
I do not actually believe that this is what the show would have looked like if O'Hare had stayed on. There are too many divergences from the story we got that have nothing much to do with Sinclair/Sheridan, that I think JMS decided to change certain things around for reasons having nothing to do with the identity of the lead character, and that would have happened just as easily if O'Hare had stayed.
The story is so big, that there's a lot left out here, and I'm sure some of the “missing” story elements were in fact included in JMS's huge pile of index cards. Most of the 7 page synopsis focuses as much on the big picture as it does on the individual characters. The only characters mentioned by name are: Sinclair, Garibaldi, Delenn, Londo, G'Kar, Kosh, and Catherine Sakai. (Notice a trend? Excepting Sakai, all of these are characters who appeared in “The Gathering”, and continued as main characters in the series. It's possible that this was written when JMS knew that the actors who played Takashima, Dr. Kyle, and Lyta were going to be unavailable, and he hadn't yet figured out how the replacement characters would fit into the story.) The characters of Santiago, Clark, and Sinclair/Delenn's son are mentioned, but no names are given for them.
One of the weirdest things is that the series seems to end on a cliffhanger, and the last page and a half of the synopsis details the storyline of a potential spinoff series, Babylon Prime, which resolves most of the major plot threads. The events in the outline seem to be in quasi-chronological order, though it's sometimes hard to tell, as there's a lot of jumping back and forth between the various threads. I've split up my synopsis of JMS's synopsis into four parts: Seasons 1 & 2, Seasons 3 & 4, Season 5, and Babylon Prime.
Here we go:
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SEASONS 1 & 2
Much of the stuff on the first two seasons matches what we actually saw on screen, including:
-Sinclair trying to figure out the hole in his mind from the Battle of the Line
-The “Babylon Squared” story
-Santiago assassination and Clark taking over
-Delenn undergoing transformation
-The Shadows slowly making their presence felt, and Londo allying with them, and Londo using them to gain influence with the Centauri
-Kosh revealing himself to all when he saves Sinclair's life at the end of Season 2
Main divergences from what we saw on screen:
-Sinclair stays on, and remains commander of the station throughout the series
-Unclear exactly when this is revealed, but the secret behind Sinclair & the Battle of the Line is not that he becomes Valen (Valen is never mentioned in this outline), but that he is the person who has been prophesied to save the Minbari from dying off. In order to fulfill the prophesy, Delenn must transform to become human and mate with Sinclair. Their son will be some kind of chosen one who will save the Minbari race from extinction(???). Some of the Minbari (warrior caste?) interpret prophesy differently, and think that Sinclair will actually lead the Minbari to doom.
-Not 100% certain on this, but it looks like the Centauri conquest of the Narn doesn't happen until early/mid-Season 3. It's also not completely clear whether there is even a Narn/Centauri war as such. The Shadows aid Londo's ascension by secretly staging a number of incidents, but does this involve a full blown Narn/Centauri war that lasts a season? Not clear. Rather, some time by mid-Season 3, the Shadows help the Centauri conquer the Narn homeworld and decapitate their empire, but I'm not sure if that's actually the culmination of a lengthy war.
SEASONS 3 & 4
-The Centauri conquer the Narn Empire with the help of the Shadows.
-After the Narn surrender, G'Kar briefly stays on B5 and tries to rally allies against the Centauri, but it doesn't work. So he returns to the Narn homeworld to join the resistance.
-Catherine Sakai is “mind-raped”, and all memory of her relationship with Sinclair is erased, and this crushes Sinclair. [This seems like some early iteration of the Anna Sheridan / Z'ha'dum story, but there's no explicit indication of how this happens to Sakai, or who's responsible.]
-Sinclair & Delenn become romantically involved, and Delenn is pregnant by the end of Season 4.
-Garibaldi returns to drinking, and resigns as chief of security. During Season 4, he's a mercenary operating out of B5, but there's no mention of the Psi Corps sleeper / William Edgars / Lise Hampton story.
-There is no mention of an overt war between the Shadows & Vorlons. But they are fighting each other by manipulating the younger races. There is no mention of an order vs. chaos ideological conflict between the two. Just that the Vorlons manipulated the younger races throughout history, and the Shadows rebel against that, and try to set themselves up as rulers of the galaxy.
SEASON 5
-The Minbari warrior caste overthrows the Grey Council, and orders the resumption of hostilities with Earth. They also want Sinclair and Delenn dead.
-The Centauri try to move in on B5's sector of space.
-Londo & the Centauri's longtime involvement with the Shadows is publicly revealed.
-The Shadows destroy a huge Vorlon ship (hundreds of miles long) which contains a large segment of their population.
-The series ends with the Minbari attacking B5 and destroying it. Sinclair & Delenn escape with their newborn baby. Everyone in the galaxy is after them for one reason or another....including Earth, which has been given info which makes them believe Sinclair is a traitor.
BABYLON PRIME
-Sinclair, Delenn, and their allies go back in time to steal Babylon 4, pulling it into the future in order to use it as a base to build a new alliance (army of light?). B4 is renamed Babylon Prime. B Prime can move through space like a starship, and they go off on a mission to clear their names and build the alliance to bring peace to the galaxy.
-The time traveling causes Sinclair, Delenn, and their baby to age rapidly. (I'll call the baby David, even though his name is never mentioned here.) David grows all the way to adulthood within a few years.
-Londo is Emperor, but controlled by a Keeper, as in the actual show.
-Londo & the Centauri capture Sinclair & Delenn, and are supposed to turn them over to the Shadows, but Londo rebels against the Keeper & the Shadows “at terrible personal cost” (doesn't say exactly what that cost is).
-David becomes a revered religious symbol.
-Conclusion of the story: B Prime and the Army of Light defeat the Shadows (but there's nothing about the Shadows leaving the galaxy). No mention of what happens to the Vorlons. Earth defeats the Minbari, and Sinclair's name is cleared. Delenn leaves Sinclair, in order to return to the Grey Council. David becomes the leader of a new interstellar alliance. Final scene is Sinclair, retired, alone on an otherwise uninhabited world....fishing.
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Plot points that are noticeably absent:
There is no mention of an Earth Civil War, or B5 seceding from Earth in Season 3 (though obviously, a lot of that storyline is transplanted into Babylon Prime). While Clark is said to be controlled by the Psi Corps, and Psi Corps is said to be a nefarious group at odds with Sinclair and B5, there's no mention of the Earth Alliance being transformed into some kind of Orwellian police state. There's no mention of the Shadows working with Psi Corps or anyone in EarthGov. There's no mention of any larger teep/normal conflict, beyond Psi Corps just wanting power for itself.
There's no mention of Sinclair going to Z'ha'dum (and in fact, no mention of Z'ha'dum), and dying there. (Though, as I speculated earlier, some of this storyline may have been there as part of the Sakai mindwipe story, but there are no details given.) There's no mention of Lorien or any other First Ones beyond the Shadows and Vorlons. There's no mention of Kosh mentoring Sinclair, or Kosh sacrificing his life. There's no mention of Marcus, or Morden, or Bester, or any other characters who I haven't already mentioned.
Still, just because something wasn't mentioned in this synopsis, doesn't mean it didn't exist in some form in JMS's lengthier treatment of the series that he kept to himself.