The game is set in Silentia, a dreamlike fantasy world that is home to a sad young circus clown named Sadwick. It opens as he wakes in his travelling circus trailer from a recurring nightmare in which he watches the world fall apart. Wandering into a nearby forest, Sadwick meets Bobby, a Chaski — a messenger of the King — who is bound for the royal castle of Corona to deliver a powerful artifact, the Whispering Stone. Bobby warns that the end of the world is near, that the land is already breaking apart, and that a hideous horde of underground creatures called the Asgil are closing in on Corona. He's been searching in vain for an oracle named Shana to shorten his journey, and asks Sadwick's help in finding her. Hoping she might interpret his nightmares, Sadwick convinces Bobby to lend him the Whispering Stone — only for Bobby to be frightened off and vanish in what Sadwick takes for an Asgil attack.
Using the Whispering Stone to open a secret passage, Sadwick reaches Shana, who reveals that his destiny is to destroy the world. She sends him to a nearby island to find the mysterious Kalida, who eventually brings him near Corona. There Sadwick stumbles upon the Asgil hideout, overhears the plans of their leader Loucaux, and is captured and jailed before escaping and boarding a flying steam locomotive to Corona. Reuniting with Bobby, he learns he's arrived too late — the king has shut himself away. Exploring the castle, Sadwick discovers a model of a planetary system tied to the flow of space and time itself, and the royal astronomer explains that the Whispering Stone represents the planet Silentia among five planets, that the ailing king must repair the system to restore balance, and that only a repaired system can activate the fountain of the Water of Life needed to wake him.