We start in the cliché forest village. Some kids went too far into the woods (where dangerous things lurk) and haven't come back. Our SamusAran-esque protagonist grabs an old sword and shield and goes after them, only to find a group of evil/monster-y soldiers (which the kids were about to get murdered by) and kicking their asses. Our heroine learns of something far more sinister slowly gripping the land by talking to the great fairy in the nearby shrine, and off she goes on her quest to do something about it.
So in the first dungeon, after completing it and helping the Great Fairie's friend/sister (either works), she is given a worn-down old staff/book/crown/set of light armor (leaning towards staff maybe but all four of these mentioned items are plot-critical ish) and is told to hunt down the rest (and the gems that go with them) so that she may stand a chance at beating the Big Bad. And away she goes.
During her travels, she comes across a relatively large town. Maybe not big enough to be called a city (because this is ZC after all), but it's still huge compared to the village from which she hails. On top of selling useful things (bought with gold pieces she's picked up from murdering all manner of foe), it is ruled by a pair of sisters.
Levana (latin for "The Rising Sun") and Nox ("of the Night") who, unknown to them or the protagonist, are really two goddesses taking on (mostly) mortal forms, who's destinies are to assist the hero vanquish the Big Bad.
In the town reside six other persons of importance. Mostly as a sidequest-ish sort of thing where they help you unlock an extra portion of previously visited (and a select few others overall) dungeons. Their names, from left to right (duh), are
Tacita, Serica, Liboria, Amalia, Volante, and Sidra. Tacita is a potion lady (who sells you potions!), Serica is a seamstress with a slight affinity for magic (who can embroider/etc. your clothes for beneficial effects!), Liboria runs/owns the inn, Amalia runs the farm, Volante is a beggar, and Sidra is an orphan who was adopted by Levana, who has immense magical ability still locked away.
So anyways, more dungeon-crawling later, the Big Bad knows shit's gonna go down so it tries to intervene from almost the beginning of the game, but about 3/4ths of the way to the end of the game, some MAJOR PLOT RELATED HAPPENINGS occur, and the sisters re-ascend into godhood while you take care of the Big Bad. I swear there's a good reason for this. <_>
That's all for now I think. It is largely a WIP but I only say that due to the possibility that it could change, but I feel like this is pretty much it. Names are subject to change.