My 5 cents...
Pythium with C'Tis (sauromancers helping the Theurgs) > Serpent cult / Pythium. Dunno in which order. Perhaps second era is about 'sauromancers are gone, but there are still some serpent temples around', and the third one is a 'pure' Pythium. At least I wouldn't like tho think that Theurg's litanias aren't offered in great Cathedrals anymore.
Desert tombs > C'Tis > Miasma, with Tombs not as a 'return of the ancient Kings' theme, but as an 'Ancient nation obsessed with Life after Death' thingy. More Egypt please.
Golden Era - Alexandria - Arcoscephale.
We have seen Arco as an old (tired) Empire and we've seen that land in its time of legends. Now its time to play a Hellinistic Empire at its prime.
Diabolical Faith / Marignon / Conquerors.
When the first waves of the Undead overwhelmed the outer defenses, great fear arose. While the most devout priests were sacrificing their live at the front lines, others were... sacrificing others lives to get help from an even more sinister source. Heresy took some time to weed off, but eventually the Inquisition was founded and succeeded in both dealing with both keeping the Death at bay and weeding out the blasphemy.
First of the Tuatha > Man > Last of the Tuatha.
Re: Dominions 3: Speculation Wars
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