The third dark fortress is in the forest in the northwest corner of the map. You will need to go to the forest in the light world and find the way to reach a removable stone that you can see from the north edge of town but you can only reach by hammering pegs on the south edge of the forest.

After getting the second crystal you have to go the man that lives in a hut in the NE corner of the light world. Give it to him and he will tell you valuable information.