From a post by Tony Bedard on Herorealm:
Y'know, maybe it's like James Dean, or Lou Gehrig -- NEGATION remains a bit special because it was cut off in its prime. It didn't live long enough to jump that old shark.
The War would have ended with Kaine luring Charon and Danik into that pocket Hell dimension called Perdition, home of Charon's old nemesis, Apollyon. They set off a special bomb designed to turn Charon and Danik back from godlike creatures into ordinary men. Then Kaine beats the hell out of both of them for causing everyone so muchy grief. We planned on him adminitering this beating with a broken toilet, oddly enough. You can see the toilet floating in space in the first issue of NEGATION WAR. Kaine would've given his puppy, Chomper, to Komptin (to make up for getting Komptin's old dog killed). Most of the fugitives would've settled down on some remote planet in Negation Space, where Appolyon would become the new Big Threat, taking apart the remnants of Charon's empire. That way, we could've followed up the War with NEGATION II: ELECTRIC BOOGALOO.
Well, I think Mordath would've turned out to be very useful and surprisingly stalwart in the battle -- sort of like Doom teaming up with Marvel heroes against some greater threat. We might've killed off Ethan. Still not sure about that, though. Ilahn from Meridian would've tried to cut his own deal with the Negation, of course. Evinlea would've survived the whole thing, even after being so bad in Charon's service. Homm...I've actually forgotten a lot of what was planned!
Oh, Sam from Sigil would've gotten killed and Kaine would've reluctantly taken command of the good guys.
I can't remember what would've happened to QZTR, but I think I planned on having someone kill him in battle. It would've been a big deal. I'm just not sure who it would've been.
Here's an interview between Ron Marz and Comic World News:
CWN: For CrossGen you created, perhaps, the strongest set of regular characters in Sojourn… a strong female lead, a believable side kick, 2ndary characters that were so well formed as to deserve their own stories and you gave the villain of the piece the “sigil”… how did you see the journey ending?
RM: With the death of the villain, Mordath. All quests have to end with the villain vanquished, right? But not in the way that would've been expected, I imagine. Arwyn was going to gather the Five Fragments of the arrow, but the whole point wasn't to reassemble the arrow and then kill Mordath with it. The gathering of the Fragments was to bring back the legendary hero, Ayden, to defeat Mordath. But by that point in the story, Ayden would have been dead. So the Fragments are gathered, but Arwyn finds out they don't do what they're supposed to do. This great, mythic savior turns out to be a useless.
But during the quest itself, the act of traveling to each of the Five Lands, Arwyn would have met enough people in the different lands to go back to them and forge an army. In the end, they rely on themselves, and not some myth, to defeat the despot. So the end would have been an epic battle, and Mordath's death in issue #50 would have come at the hands not of Arwyn, but of Bohr, the troll who once served him.
I feel vaguely robbed all over again now. *pouts*