Well I'd be the first to admit I haven't been hands on with Warhammer Lore for a number of years but the Scalies have always been one of my favorite races.
They've been thrown out there as a idea a few times for a playable race a few times but lorewise they'd be a fairly shaky fit, the idea of them buddying up with other races just dosen't seem to fit.
First a page from Games Work about Lizardmen, general kind of info. Easier for me to link it here and refer back to it.
But I think it could be made to work leaving the Warhammer Lore perhaps a little bent out of shape but by no means broken.
So I'm taken a giant leap and guessing the Red Plague is hopefully the sign of a Live Event, proberbly a three parter leading up to a proper expantion, as a starting point.
The event would lead up to a new zone being Lustria and the tunnels stringing from there through to Skavenblight or one of the other Skeven Cities. With any luck this would also be a great time to reindroduce the new cities for the other racial pairings. (Considering they were planned out and partly done during the run up to release implimenting the Elven/Elven and Greenskin/Dwarfs cities should be the easy part)
So it would start with the Red Plague being released upon the old world, disease strikes across the Old World released by the Skaven hordes forced into a pact with the Chaos forces. This would be easy enough Lore worse, I don't think you'd put Skaven anywhere but squarly on the side of Destruction. As the Order forces pull back to fortified positions and cities giving the forces of Destruction the opportunaty to show their hand. The Raven Host splits some staying behind to harass the Order forces and keeping them off guard the rest boarding a fleet of Choas Warship sailing for the New World and the lands of Lustria to join forces with House Uthorin reservists marching South from Naggaorth and Greenskin forces emerging from the old abandoned tunnels from which the Skaven first crossed into the New World centeries ago. The forces gathered they sunder the Wardings that kept these tunnels impassable to Skaven and the Ratmen emerge to swell the host.
(No clue is that would work, sure I read somewhere that the Skaven were driven out of Lustria and kept out somehow, if it was Magical wards then it would work, barriers battered by Dark Elf magic from outside and Goblin Waaagh from within, if it was something more boring like "collapsed tunnels" then the Goblins can lug picks and blasting powder with them!)
The reasons for the subtifuge? Well quoted from Games Workshop that link above:
>In the wake of the Old Ones
Left alone and vastly outnumbered by the Daemons of Chaos, the Lizardmen valiantly defended their temple-cities, each fortified against assault and protected by the magical power of the Slann Mage-Priests within. Still the Daemons wrought untold carnage on the Lizardmen, knowing that should they destroy the network of temple-cities and break the geomantic web that ordered the ebb and flow of magic upon the world, Chaos would reign.
That would be reason enough for Chaos to go at it, the Changer of Ways likes to keep a lot of plates spinning at the same time and cracking the "geomantic web" would work. The rest of Destruction would be their either as Allies or to hunt down a lost Macguffin-Of-Awesome-Power in the case of the Dark Elves.
This is in danger of becoming a stupidly long wall of text so I'm gonna go for to be continued and to the Order/Lizardman thing in a follow up post. Yeah I know the Lizardman thing was the whole reason for this in the first place but I got carried away. I write it up tonight and post tomorrow most likely!