New theory:

The Metaverse villain is Morgana, or rather, Morgana is the fractured soul of that person (possibly a Persona? Igor mentioned the black masked user can also use multiple personas). Either the goodness in them left to seek out a way to turn them from evil, or something happened to remove Morgana from them and that's why they're doing evil trout in the Metaverse.

anyways, that's my guess