I figured out the rest of where Phantasy Star Online fits into things. It obviously takes place after The End of the Millennium — perhaps a thousand years, to follow the series trend. Yet the disturbance in this game is related to PSIII, namely the piece of Dark Force that was on the ship Alisia. Unlike all the “major” manifestations of Dark Force, back in Algol, that Dark Force wasn’t destroyed. Further, at the end of the game it did supposedly vow to return in a thousand years.

What I’m thinking then is that somehow the residents of the ship must have buried him on Ragol. Then a couple of thousand years later (a thousand years after EotM), when the rest of the Algonians escaped Algol on the Pioneer ships, they just happen to take the same route as the earlier pilgrims and so find the Dark Force that was left behind by their distant relatives.

Just figured I needed to write this down where I might be able to find it again later.