About 1000 years ago the earth suddenly died. While the earth was in its death throws a clockmaker known as Y stepped forth and rebuilt the world into one gigantic mechanical uhhh well I guess clock and humanity was saved and now lives on this giant clock. One day Naoto is just minding his own business when a large container crashes into his building. Inside is a beautiful automaton that Y built. Naoto fixed up RyuZU and in doing so gained himself a servant. They team up with a random genius clockmaker and travel the world maintaining the slowly dying clockwork planet.