I presume you're talking about a one-off adventure for an existing campaign.
And continuing that presumption, I'm running with the premise that despite the magical big bad wanting the characters dead because they "know too much", because you're asking for ideas about codifying that big bad the players of course have no pre-existing inkling that the big bad is out there wanting them dead.
Bug spirits are great, but if you haven't already been foreshadowing/using them, they're hard to suddenly jam in and pretend they've always been there.
Vampires work great in this way. Not only are they sneaky like that, it's naturally easy to rationalize prior encounters/events as having secretly been linked to the coven even without the players/characters ever realizing it. (remains to be explained, however, why the Vampires think the runners know so much when they don't)
If you want to go full bore Shadowrun cliche, make the big bad an honest to goodness dragon. They work through pawns, and hell the Vampire Coven could in turn have themselves unknowingly been manipulated by the dragon, several steps above them on the organizational chart they didn't evn know they were on!