The 3 ancients would be either stage hazards or bosses.
It's a Nintendo game, and I don't think it would need to be toned down too much to make it into Smash. (any stage seems like it would be unsettling and creepy rather than outright gory, with sanity effects that are designed to mess with the player as opposed to being gruesome) You could have Alexandra Roivas (the main protagonist) or Pious Augustus (the main villain) as playable characters - I'm not sure how likely it is that this guy would make it into the roster alongside Mario or Kirby:
...but if he is a bit much, Alexandra would be a safer option. (I already wrote a moveset for her, and Pious would be similar since they use the same magick system, as the game calls it)
(For bosses, fight them one by one in a 3-phase battle)
Edit: These three eldritch horrors.