This is just the introduction to the story. Sort of sums up a little of what we already know and a bit I put in there (because that's what fan fics are about). The second chapter is where we get into everything.
In the 19th Century, there was a partnership. This partnership was between Nicholas Flamel and a strange man called Albus Dumbledore. Dumbledore was undeniably the most unusaul man the Alchemyst had met, he talked of things that were impossible. Flamel had trusted this man with one of the most hidden secrets in human history
Nicholas told the Wizard man the secret of the philosopher's stone, and Dumbledore set out to change it. Albus had a plan in his head, to have a philosopher's stone hidden away for any time he might need it.
Flamel hated the idea. Having the stone, even in a safe place, for more time than it was needed was a danger. And he was right. Over time, stories started growing about the stone. People now thought it could do anything, grant wishes, destroy worlds, much more than it's usual task of turning metal into gold and common stones into jewels.
It was now a tool thought to do unimaginable things, though it could not do them. Dumbledore put extra measures in place to guard the stone and eventually, over a hundred years later, got a guard dog.
Flamel was still weary of the dangers and abandoned the Professor when Dee was back on his trail. And the two didn't speak for over a century.