Clockwork Knight 2 is the second game featuring the adventures of Sir Tongara de Pepperouchau III. It has the same gameplay style (a mixture of 2D side-scrolling platformer with 3D elements) as its predecessor and Bug!. The story continues directly after the events of the first game: the brave hero has rescued Princess Chelsea, but she doesn't wake up. As the toys try to figure out how to solve this problem, the princess is kidnapped once again, and Pepper embarks on a journey to save her.
There are some minor additions to the gameplay formula, such as collectible cards scattered through the stages, forced side-scrolling levels in which Pepper rides his horse Barobaro who shoots projectiles from his head, and a mode that allows the player to fight all the bosses from both this game and the previous one.