In 1998, a special edition was aired on to kick reruns of the Babylon 5 series. The Special Edition (1998) has a new score by Christopher Franke (of the regular series), cuts out small bits like the "zoo scene" at the beginning, corrects effects like the color of the jumpgate, and adds a few scenes which were cut out: Sinclair deals with a hostage situation in customs involving "dust"; Carolyn confronts Delenn about her abstention on the vote; the Takashima and Kyle scene is extended, as is the scene where Sinclair describes the Battle of the Line; there's a new voiceover with Kosh's voice; plus Kyle remarks on what he saw when he opened Kosh's encounter suit and the mystery of Kosh's hand is hinted at (longtime viewers will get it; new viewers will just say, "huh?" so the mystery won't be spoiled.)

The original PTEN airing of the film did not include The Gathering as part of the title; it was simply called Babylon 5. The Gathering was added for future airings (the special edition).

In the original airing, the end credits scroll over a hand-drawn sketch of Babylon 5. This is changed in the special edition by replacing the original credit scrawl with one that matches the end credit scrawl of all the episodes and telemovies.

Londo Mollari: I was there at the dawn of the third age of mankind. It began in the Earth year 2257 with the last of the Bablyon stations located deep in neutral space. It was a port of call for refugees, smugglers, businessmen, diplomats, and travelers from a hundred worlds. It could be a dangerous place, but we accepted the risk because Babylon 5 was our last, best hope for peace. Under the leadership of its final commander, Babylon 5 was a dream given form. A dream of a galaxy without war, where species could live side-by-side in mutual respect. A dream that was endangered as never before by one man on a mission of destruction. Babylon 5 was the last of the Babylon stations. This is its story.

Londo Mollari: There was a time when this whole quadrant belonged to us! What are we now? Twelve worlds and a thousand monuments to past glories. Living off memories and stories, and selling trinkets. My god, man! We've become a tourist attraction. "See the great Centauri Republic - open 9 to 5 - Earth time."

Delenn: I look forward to meeting a Vorlon. I've heard much about them that is strange.

Jeffrey Sinclair: Such as?

Delenn: Do you not have files on the Vorlons?

Jeffrey Sinclair: Absolutely, very large files. There's nothing in them, of course.