Alright I got all three crystals in The Stout Mines and am at a part where one of the crystals where in a chest right behind the rock. What do I do now and where do I go?

You're in Dragon Spire, aren't you?

The dragonshards need to be placed on an dragon emblem which I think is to be found south of the highest bridge. Placing the shards on the emblem will open a door behind you.

Wyv