Yoyoyo!

The Fathercrystal just disappeared from the story and we didn't see it in 6.0. I hear people claim it's beneath the Zodiark fight arena, but I never saw it myself.

I think the reason why they didn't wanna show more of the Lunar Subterrane dungeon in the Live Letter (Yoshi said it would be too spoilery) is because we'll see the Fathercrystal there at the end.