Xenosaga Episode III: Also Sprach Zarathustra

first off, there is no use of the geocrystal outside of acquiring shion's ultimate weapon, and I'm not sure exactly what secret level you're talking about, but i'm assuming it's the one where you first exit the E.S's on the floating landmass? If so, you need to go all the way back through the area (easy if you came here through the UMN). when you get to the coffin at the end, go around behind the cross to find a hidden door. there is a second coffin and there's an acadian resource special item on it, gather it and put it in the slot on the pedestal. The dungeon is long, tedious, and not really worth the rewards, but I think you have to do it to complete the database.

if this is the right dungeon, then i hope this helps, if not, be more clear. As to finding the Geocrystal, I answered that already, on the other question you posted.