I figure this is the perfect thing for the middle part of the module. Tell me whatcha think, it's from some of the ideas I've seen here earlier.
Trial of a God
The PCs, after settling up the adventure-hooks in Sigil, are lead down to the headquarters of the Athar at the base of the Spire. There, they find the Faction is in a bit of a state of an uproar over events that have occurred recently.
The Alchemists of the Athar's Militant Faction working with some Doomguard artificers (I suggest a guest appearance by Coaxmantle from Planescape: Torment) have used the peculiar metal from the base of the Spire to create Godkiller. The Magical Rod/Staff/Sword or what not that can defeat deity.
My suggested write up for it is here. http://www.planewalker.com/forum
They've successfully managed to sever a carefully selected Minor Deity just clinging to Powerdom from his remaining followers. Even this small act has caused massive ripples throughout the Planes are just smaller than Orcus' using of the Last Word. Even worse, the deity Grinforr actually tracked it back to the Athar and attacked them. This has lead to the peculiar situation where the Athar ended up capturing a god.
About half of the Athar are simply paralyzed with indecision over what to do with this issue with some of the more bloodthirsty or fearsome just wanting them to destroy the god outright. Others wish to see the deity let loose in the vague idea that he won't harm them (these are largely shouted down since, well, the Athar are a bunch of cynics by nature and Grinforr is an evil deity).
The Militant Faction's leader, Trent Castellan, has decided to make a Show Trial of the God and bring him to task for his numerous crimes against his worshipers. He believes, correctly, this will become a tremendously famous act after the fact.
How the PCs get there
We can also insert rumors that many mystics across the Multiverse felt something of a brief stirring while there were things like Earthquakes and other natural disasters that should be impossible on the Githyanki's Dead God's bodies.
But yes, definitely the first part of the module should get the PCs down there. They need to make contact with an Athar sponsor to get past the heavy defenses of the Athar though and probably should make some friends in the module's first section (Blowing up the Temple of Hades here http://www.planewalker.com/forum for befriending the Militant Faction or probably helping the Moderates in some other adventure hook).
Factol Jaya Forlorn: Is mostly trying to balance the two factions and is interested in seeing where this plays out. She's subtly encouraged Caymean to sabotage the Godkiller Project and hopes that the trial will somehow backfire and destroy Trent's credibility.
At present, she remains the "moderate" influence.
Trent Castellan: The Leader of the Militant Faction and the one who has come up with the Trial Idea. He'll try and persuade PCs to participate in the Trial with acceptance from any who want to play Lawyer.
(It might be interesting to have a Rimalli be the judge)
He also wants the PCs to get Godkiller away from the place along with the notes on how to manufacture it in the Astral Plane.
Caymean: The Tiefling leader of the Moderates pretty much wants to do anything he can to get Godkiller destroyed and the notes for making the Process destroyed. He's less concerned about Grinforr's security even as he believes the damage is more or less done.
Though he wants the monster to have a good "defense" and possible acquittal to mitigate divine vengeance. It's not helped by the fact that Grinforr is guilty as sin.
Grinforr: Grinforr fully intends to escape during this Trial and kill as many Athar as possible before escaping with the Godkiller. The monster believes, correctly, that there are both Demon Princes and Gods that will both pay handsomely in exchange for it. He's certain that one or more or them would restore his divinity in exchange for it.
He's already convinced a few of the Athar to collaborate with a jailbreak.
Someone gets away with Godskiller and the final results of it will largely help determine who becomes Factol after Jaya. Though later events in the story will still have an effect, the results of this trial will be a major determinant in the adventure's next status.