Access Shadow Tower:
In order to access the hidden shadow tower you first need to get the dark crystal. After you get the dark crystal go to any save point in the game and access the items menu (first choose the top option which will bring you to the orange menu and then you choose the second option to use an item) and simply just try and use the dark crystal. In case you were wondering it's a crystal that looks just like the save crystal and when you try to use it, it will ask you if you want to go to shadow tower. For every dark crystal you get you will be able to make one trip to shadow tower.