Continuing my series attempting to reconstruct how Babylon 5 was originally (for certain values of original) "supposed to" go. More detailed explanation and Season 1 are here, although note that since writing that original post I have gotten access to JMS' "original" treatment and am no longer working from summaries.
Known: Season 5 opens with the return of G'Kar with evidence of Londo's alliance with the Shadows and their meddling in the Centauri-Narn conflict. The Minbari military caste stage a coup and take over, resuming the war with Earth. The Centauri lay claim to the neutral sector that includes B5, which Earth contests, leading Londo to break off diplomatic relations. Shortly thereafter a massive Vorlon ship carrying most of their civilian population is destroyed by the Shadows, although Earth is framed. Londo helps in the attack, though without the knowledge that it will result in hundreds of thousands of innocent deaths.
The series ends (yes, ends) with the Minbari attacking and destroying Babylon 5. Sinclair, Delenn, and their baby escape on a shuttle and flee into hiding, with every remaining power in the galaxy considering them enemies: the Minbari because of Delenn's ties to the deposed Grey Council and the Warrior Caste's belief that the prophecy is one of destruction, Vorlons because they believe Sinclair helped Earth destroy their ship, Shadows and Londo because they believe Sinclair and Delenn suspect who really did it, and Earth because they've been fed false intel that Sinclair betrayed them.
Speculation: Given how much happens in this season, and how little happens in Season 4, it seems likely that some of this would have been moved earlier. Any of a Centauri attack on Babylon 5 as part of them seizing the sector, the fall of the Grey Council, or the destruction of the Vorlons would have made good season finale material (though the last might be too soon for the war to end in this version of the story).
Given his human-Minbari hybrid wife and the renewal of Earth-Minbari hostilities, it seems likely that Earthgov's false intel makes Sinclair out to have betrayed them to the Minbari. Likely sources for the intel are the Minbari, Centauri, and Shadows, all of which have good reason to want to isolate Sinclair and Delenn and thereby cut them off from Earth support.
It's up for grabs whether the warrior caste are being manipulated by the Shadows in this version of the story. They almost certainly weren't in the actual series, but by this point the treatment and the show have nothing in common except Delenn's pregnancy.
And yes, this colossal downer really is how the series ends in the treatment. But it's not how the treatment ends--that still has another page and a half, almost a quarter of its length, to go. We'll cover that in the next and final installment of this series.
Concluded next week!