To unlock Clockwork's Time Quest/Mission Mode, simply beat the game once on Normal difficulty. Once you do, go back to your saved game and Clockwork himself will fill you in on the rest. Then you're in Mission Mode. In this mode, you can also fight enemies from the past such as Skulker, Ember, and even The Box Ghost. This mode also has you do different things on the past levels to earn medals such as "Do NOT Use Plasma Powers" or "Beat 5 ghosts in under 30 seconds."