the zombies

[Enkidoh]

That defeated city-state is Sil'dih, and in 1.0 it was indeed stated that during a war with Ul'dah (over water supplies during a time of severe drought if I remember rightly), Sil'dih (who were losing the war), indeed resorted to necromancy (ala, reviving their deceased soldiers as undead warriors) Naturally, this backfired on them horribly, and the magc that the Sil'dihian mages were using to revive the dead soldiers also spread to the civilian population, resulting in a zombie apocalypse. Ul'dah used it to their advantage, turning the purpose of the war as an excuse to wipe out Sil'dih to 'send these abominations back to Thal', and by the end of it, Sil'dih was sealed off completely, trapping the living, dead and undead together.

In ARR the ruins of Sil'dih have actually started being unearthed - there's a section of Central Thanalan called 'the Sil'dih Excavation Site' found along the path to Western Thanalan - there's not much there really - just a jumble of broken stonework found at the bottom of a deep gorge. Interestingly though, the only mobs found there at the moment are not undead like you might expect, but spriggan graverobbers - graverobbers? Hmmm....

It should also be noted the whole affair with Sil'dih ironically resulted in necromancy getting a bad reputation in Ul'dah - the THM's Guild flatly refuses to dabble in such dark arts (if I remember rightly this was mentioned during 1.0's original Ul'dah story where it had a connection to the narrative). In any event, although the fate of Sil'dih does neatly explain the cause of the zombies found in Thanalan, it doesn't explain undead found elsewhere, such is in the Tam-Tara Deepcroft in the Black Shroud. Unless the magic employed by Sil'dih is far older and more widespread than first thought.