Covering the rest of the story, I have to say that I'm impressed with the ideas that make up the plot. Many of them are unique, or done in a refreshing manner. There are a couple of things that prevent this from being one of the truly great pieces of fiction in this fandom, though. One is the spelling and grammar. One or two errors that were missed in editing can be easily ignored, however this story is full of them, and it really detracts from the story you're telling. Don't rely entirely on spell-check, because it is far from fool-proof.
The second is the pace. Things simply happen much too fast. A quick pace isn't necessarily a bad thing, but here it's too the point of things being unrealistic. For example, in my review of chapter one, the intimacy between Magus and Flea comes about so quickly, that I automatically assumed that Flea was using the charm spell as a part of some master plan. Yes an attraction between the two of them had been mentioned, but as something that was in their past, plus Flea is assumedly still getting over the death of her lover, Slash. You can build it up again, but give them time to interact.
The final thing was that you made canon adjustment/assumptions without giving explanations. The two things I'm thinking of here are the pendant and the gates. The gates are something that are often left functional in fanon, but canon says they were becoming unstable at the end of the game. At least a token mention of them having stablized again should be made if you want to use them.
As for the pendant, it's never said that it's in the royal family in 600 AD. Queen Leene's heirloom is her coral brooch. Again, that doesn't mean it isn't there, but an explanation of its presence should be made, at least in passing. Maybe she doesn't wear it much, maybe it was a recent gift, etc.
(A chapter three specific nitpick: I think you said Choras when you meant San Dorino. Not too big a deal, but a bit confusing.)
You really do have a great story here that just needs to be touched up to truly shine. The ideas are fresh, the character interactions fun, and there really are some great lines and moments. If you'd like, I could e-mail you some detailed C&C similar to what I did for the first chapter.
It'll be interesting to see where you take this story next!