You begin as a rather ugly man named "Beethro" who travels deep beneath the ground. There are other people down there too, citizens of a mysterious "Rooted Empire", that are carving tunnels and building things. Beethro just wants to know why, but it's hard to get a useful answer. He was always fond of saying "there is no problem that can't be solved with a really big sword," but upon arriving at the underground capital, Beethro is startled to find that nobody seems interested in attacking him. No, for some reason, they would rather persuade him to stand in a very long line.

The story picks up roughly a year after Journey to Rooted Hold ended, with Beethro arriving at the mysterious Rooted Hold and exploring an underground city of the Empire in search of his lost nephew, Halph. Soon, Beethro discovers a sinister plot concerning all the people above, so finding Halph and convincing him to return home becomes a second priority. It is up to Beethro to foil the Empire's plans and discover its most guarded secrets.