So take the Goa'uld from Stargate and combine a bit of Harry Potter magic with shadow magic and dump it in Domino Japan and laugh evilly as it all plays out...
(All characters belong to their original creators who are gracious enough to let us reek havoc with their babies.)
In a world of magic and aliens the Goa'uld Sun God Ra ruled Ancient Egypt with an iron fist. The first to discover the Tau'ri, Ra was the one, and the only, Goa'uld to ever be able to use shadow magic. The other System Lords could not understand it. They would spend countless days, weeks, years trying to track down the elusive shadow magic users to claim them as hosts. They would possess these humans who had shown their ability to use shadow magic, but could never unlock the magic for themselves. What they didn't realise was you had to cultivate shadow magic yourself, eventually splitting your soul, using Ka to create a spirit monster that reflected yourself like nothing else could.
Ra protected as many as he could, not out of love or a twisted sense of duty but merely to keep the secret to himself, to make sure he was the only Goa'uld with the rare talent. He made sure no one with shadow magic was able to get through the Chappa'ai keeping the secret to the first world, preventing it from spreading across the stars. As time wore on this became more difficult so from the shadows Ra manipulated the humans of the Tau'ri, helping them in their quest to overthrow the 'false gods'. He would loose the planet along with the other System Lords, but he had Abydos and the others to make up for it.
In time the Goa'uld forgot about the mysteries of shadow magic, fading from rumour to whispers, eventually falling into silence, remembered only by Ra. The Tau'ri buried the Chappa'ai, slowly healing from the wounds caused by their evil overlords, real experiences recalled as myths and legends, remembering the what but not the why. They remembered shadow magic longer than the Goa'uld, but in time the knowledge was buried just as knowledge of the Chappa'ai was before it.
So I'm full of shit and making this up as I go along. I have no idea how the timeline works with this thing, events just happen *shrugs*. So each Duel Monster is half of someone from the past's soul, the more people to use shadow magic the more half souls out there...Let me know what you think...