Harry Potter, up until Christmas First Year, has had a fairly normal Hogwarts experience (for him at least). Then everything changes the first, and only, time he goes to visit the restricted section.
For there are books most invisible, as suggested by the existance of the ever elusive Invisible Book of Invisibility that exists, somewhere, in Flourish and Blotts.
And Harry Potter just happens to stumble across an Invisible Book in the restricted section. One he would not have been able to find, let alone see, if not for the fact that he's the first heir of *two* founders to stumble across the area.
And thus he finds an inocuous book, with the strange title marking it as 'The Akashic Tome'. Taking it, he finds nothing but a forward inside and a 'table of contents' displaying what books it has, and how to access them via your will (aka wandless magic). And what's in it? Why, a book from each of the four founders.
The Thaumonomicon (Salazar Slytherin)
The Lexica Botanica (Helga Hufflepuff)
The Sanguine Scientiem (Rowena Ravenclaw)
The Astral Tome (Godric Gryffindor)
The foreward explains that even in the day of the founders, these magics were rare to the point of being regarded as myth. Even Merlin only had access to the Astral Tome, which was a large part of the key to his claim to fame even today.
Alas, by the time the founders came to find that they each had the *very last of these books in existence*, most everything needed to excel in each area was gone, with only little bits and pieces here and there, with Hogwarts Come and Go room as well as Salazar's chamber of secrets serving as a repository of what little they were able to find, and with Hogwarts serving as such a focal point, it took very little time before the idea of it becoming a school to pass on what little is left came about, and thus it happened. (though unfortunately in the end, Slytherin would be driven mad by the Warp and result in the legend of Gryfindor VS Slytherin that exists today). Now, all that's left is just a few things that might spark off the bringing back of these magics if done correctly, and thanks to prophecy, this book has been combined by the Founders to be used by the one who will bring the magics back to the worlds. Hopefully by the time their prophesied one gets the book, the last Thaumic Aura Node in the Chamber of Secrets and the last Astral Collector Crystal located in a special 'outdoor' version of the Room of Requirement (then known as the Postulationem Autem Locus) would be charged enough to be of use.
Unfortunately redstone no longer exists, and it's determined that delving into blood magic would require such, for the very first thing needed to access anything is to capture demonic will with a rudimentary snare, with which to make a blood altar, as well as a block of redstone, which is required to make an Apprentice's blood orb. The rudimentary snare requires redstone.
Thankfully Ravenclaw also had her own private room in the Postulationem Autem Locus where she had a long term magical array transmuting various magics and items into a single pile of redstone, which could be duplicated via mana.
Unfortunately mystical flowers no longer exist, so delving into Botanic Magics is also impossible.
Thankfully, Helga Hufflepuff was not the world's premiere (if only) magical botanist for nothing, and was able to create a magical array powered via the ambient life magics of Hogwarts (particularly since it became a hub of such thanks to students being abundant with it since it became a school) which eventually grew and turned into the Forbidden Forest, which would, eventually, spawn one single mystical flower, which could then be used to make floral fertilizer to make even more.
Since the Forbidden Forest is particularly susceptible to dangers, what with being unhidden without the school (as it needed to be), the four founders worked to raise/develop a defense for the precious array hidden out in the open. To this end, the Centaurs, then a race of non magical creatures, were raised via Godric's and Helga's rudimentary control of Astral and Botanical magics to understand the stars and have a connection with nature to be able to see when the one who would bring the magics back to the world would come for the flower, and use the forest itself as a defense if necessary.
As another defense, this time for the things within as well as without the castle, both Salazar and Rowena combined their known magics of blood and Thaumic to create a race of living golems that require a bond to a mage to maintain life. Thus the first House Elves were created.
Then Salazar went crazy due to the warp and added a freaking Basalisk to defend the chamber and blocked access to the Chamber from the House Elves as well.
And thus we have the start of the setting leading to Harry Potter being the chosen one leading to the recreation of Thaumic, Sanguine, Botanical, and Astral magics and bringing them back into the world.
I think this could be a really cool fic.
(the shards need to be recreated. I figure that's something also in the Chamber of Secrets that Salazar conceived of in his warp addled mind, using the last aura node and alchemy to distill and create shards from Vis. Which would also slow down the magics trying to make the aura node more useful, meaning it would have the standard low vis amount of a normal node. As for a lack of Sinister Nodes and Obelisks… I think that would require a bit of finagling with magical portals from all the magics maybe… I mean, technically aura nodes ARE just tiny gateways to a realm of pure magic or something…)