When you first gain access to the Clock Tower, you can't get very far. Using your new Wolf Form, you can grab a few items, but you'll have to come back later to explore more thoroughly.
Once you can turn into a Bat, you can explore the rest of the Clock Tower. Truth be told, there's nothing here that's vital to your quest, though the Fire of BatRelic is useful and easy to get.
You can break the right wall at the top of the leftmost Clock Tower shaft to access a hidden area. There is another hidden room that opens only when you find the four gears indicated on the map and set them all correctly. To set a gear, hit it with any Weapon. It is set correctly when it makes a clicking sound instead of the usual heavy noise.