In Clockmaker, you have to help the heroes save the towns of Clocksville and Darkchester from the main villain, the Clockmaker, who has stolen the townspeople's time. In the company of Uncle and other characters, save the town and its residents from the Clockmaker's curse.
To progress through the main game, you need to lift the curse from each building in the two towns. You lift the curse from a building when you assemble all the necessary items, which drop when you complete match-3 levels. As soon as you collect enough items for a particular building, you can lift the curse from it and move on in the game's story.