I think that would be a great idea, and it would also let you implement some sort of "Planetary Bombardment" feature aswell. Not sure how you would code this but il leave that to the experts (im a Python noob!).
An idea how the story plays:
"An Imperial Grand Battleship crash lands on <this planet> (which is still un-named by the way

) after a warp storm scattered the rest of the fleet. On landing, they find a world just heading towards the civilized state of afffairs, with lots of human (or otherwise) tribes competing for resources, techs ,etc. Then , in the midst of the same warp storm that brought the ship to <this planet>, a Chaos fleet lands and starts attempting to unleash some sort of Greater Daemon using a rare ancient artefact found only on this planet (generic i know but it fits in with the theme of Chaos Incursions, and gives you chance for the Eldar and Dark Eldar to make an appearance later on

). The Imperial discovering this decide it is their duty to stop Chaos from achieving the Summoning, and so try and set up a forwards base from which to fight The Great Enemy. However they didnt count on some of the tribal leaders seeing the benefits of the Chaos Powers and so must fight them. The tribes themselves aim is to (typically) gain as big and best an empire as they can, using this period of strife to propel their people forward in whatever way they can.
The system wide Armageddon struggle goes on but the people of <his planet> are oblivious except on the rare occasion when the warp storm abates and Imperial fleets get a fleeting grip on the area..."
How this would play out:
Imperial civ automatically assigned Imperium "Religion" (locked for game entirety)
Chaos civ automatically assigned Chaos "Religion" (locked for game entirety)
50/50 split between Tribes who is assigned what religion
OR
Python makes a check on each civ to decide their "religion" at game start.
(tribes can switch at any time after researching/encoutering each religion).
This story would open up a new type of victory (Summoning Victory) so that whoever controlled the Artefact after a certain number of turns wins. This would only apply to the Imperial (after certain number of turns warp storm flares and then dies without incantations being chanted) or Chaos (at critical warp-storm-flare time incantations successful and Greater Daemon is summoned)
To make up for this, tribes also get a new victory condition only avaliable to them (Planetary Domination). If a tribe conquers 70% of land and population (or whatever number) they win, to signify their absolute control of the region (very very similar to normal domination, except it is disabled to Imperial and Chaso- they are only interested in the Artefact).
This would also give you the chance to incorporate Eldar and their Dark brethren at a later date if you felt that was necessary and not too much work. (i like the idea, as they generally get involved in this sort of artefact control thing).
These are just ideas iv had about the mod, and i submit them in absolute humility. I will not be offended if you turn around and say "these ideas are rubbish, go off and help some other poor sap"

.
But please dont
mrkingkong