I hate to start out C&C with a criticism, but wasn't Magus' castle destroyed when he summoned Lavos? Afterwards there's just a huge pit there... Maybe if you make it the ruins of his castle, or a new lair?
Interesting take on the Ozzie side-quest. I don't think I've seen it portrayed like that before.
["Magus shrugged. "Not particularly. You may have a use to me yet. And if not..."]
There's an extraneous quotation mark at the beginning of this.
I like how you didn't make the top trio in the game the top trio in the past. Makes sense that they'd have to work their way up to the positions they reach by 600 AD.
Magus admitting defeat and calling for help before he's even seen the creature seems a bit out of character to me. If anything, I'd say he'd be more likely to be over confident and get himself in trouble than to call for help from Frog so easily.
You say the monster's eyes are colourless. Does that mean they are clear, or white? Or black, if there's no irises?
[Inhuman and non-Mystic, he was a loner, and while a part of him didn't mind this, another, more sentimental part of him he had hidden deep inside long ago longed for contact he had been unwilling to allow himself.]
I like this line a lot. Especially the "Inhuman and non-Mystic" part. Poor Magus doesn't really fit in anywhere.
[The last few minutes were a blur to It, the last thing It could remember being that powerful mage casting some sort of incantation.]
"Being" might sound better if you change it to "was". Even better would be if you split the sentence into two smaller onces. It's a bit awkward right now.
[It wasn't quite as powerful as the vortex summoned by the gurus and controlled by the King Zeal]
Should be "by the King of Zeal" or "by King Zeal".
[...but now, after centuries of consuming lesser demons, monsters, and other magic beings, Its power and experience were a thousandfold of what they had been before Its imprisonment.]
Wasn't it just freed? Or is this another plot point that I'll learn the answer to later?
[As long as their was magic on this plane]
"Their" should be "there".
[Flea was convinced that the Black Hole had destroyed the thing or cost it into oblivion]
"Cost" should be "had cast".
When they're leaving the island, both are magic users so they could fly or teleport off the island. They're not really restricted to just one exit. If you want to make a reason why they have to go to the Magic Cave, perhaps mention some kind of magical warding around the shoreline?
[Once Magus had reached the age of nineteen years he began to motive a change in Flea's behavior.]
"Motive should be "notice"
Major bugging eyes at the last bit of this chapter. I'm assuming at the moment that Flea cast charm, but I guess I'll find out, won't I? ^_^
If I ask a question, or point out an "inconsistancy" that will be explained later, feel free to just say "you'll see". And everything here is just my view. If you disagree, it's your story, and you don't have to agree with the opinion of a reader. I hope this helped some, though!