When Zen, the son of a doctor, takes his dog for an evening stroll, he finds himself unsuspectedly stranded underground, surrounded by Mudbutts, odd little creatures whose livelihood and home are in danger. Zen must find a cure for the Mudbutt’s general, Mr. Beets, or he may never see his home again.

Queen Ruthaless is on the warpath to Mudbutter, the only underground city that remains unclaimed by her regime. Our story begins in one of her dungeons where Mr. Beets, our hero, and a Mudbutt, is captured. Queen Ruthaless knows Mr. Beets holds a secret to opening and closing the gates of Mudbutter, and she aims to find out what it is. His torturer, The Tickler, tries for several hours to break Mr. Beets mentally and physically by subjecting him to the smell of raw onions and tickles to no avail. Tired of waiting, Queen Ruthaless takes matters into her own hands by injecting a curse into Mr. Beets. A struggle ensues, and Mr. Beets escapes her clutches, but not before the cursed needle unconsciously pricks him. Unaware of the curse, Mr. Beets flees to Mudbutter, thinking he has thwarted Ruthaless’ evil attempts.
Meanwhile, above ground, Zen, a nerdy thirteen-year-old and an aspiring pharmacist, wakes up in the middle of the night to let his Rhodesian Ridgeback out to relieve himself. Unaware his forgetful father had left the main gate open, his quiet trip in the night turns into a full-on dog chase. He catches up with his curious dog; Zen clumsily trips over the leash, knocking himself unconscious. When he comes to, he realizes he is in an underground tunnel of Mudbutter with two non-human creatures and the permeating odor of a very smelly sock.

As Zen establishes trust with the creatures, he realizes that all the logical ways of getting above ground are closed. Reluctantly, he tries to persuade the creatures, Loity and Stockie, to show him another way and learns that there is a more dangerous creature called Dhakara that inhabits the tunnels. Evacuations are underway in Mudbutter now that Queen Ruthaless is trying to attack the city. Loity and Stockie believe that Mr. Beets is the only one who can stop the mayhem. To their distress, however, Mr. Beets has been hospitalized due to his injuries. To avoid isolation in the tunnels, Zen tags along with Loity and Stockie under the pretense that he will be able to treat Mr. Beets, a patient under the care of Dr. Iris.

After an unforeseen, life-threatening adventure in the tunnel, Zen has a chance to escape the underworld. However, he feels obligated to assist Loity and Stockie since they extend Zen hope and save his life during their adventures. The trio advances to Dr. Iris’ cavern, and Zen learns that the key to stopping Queen Ruthaless’s invasion lies within Mr. Beets. As Zen tries to diagnose and treat Mr. Beets, the challenges posed by his surroundings and location come to light. The Mudbutts and Zen also learn of a traitor sent by the queen to seal Mr. Beet's fate.
It takes some time, but Zen tactfully overcomes the challenges and successfully revives Mr. Beets from his stupor. As Mr. Beets comes to his senses, Mudbutter’s tunnels echo with Ruthaless’ war sirens. Mr. Beets quickly assembles a team to face Ruthaless’ army. Battling their way to the control room, the team learns of the conspiracy Ruthaless planned for them. An epic battle begins as Mudbutts and the queen’s army clash.

Amidst the battle, with Zen’s help and Stockie’s quick thinking, Mr. Beets gets to the control room in the nick of time and saves the day. Even though Mudbutter is victorious, Mr. Beets receives bittersweet news that his ailment is permanent. Zen provides insight, entrusts Dr. Iris with Mr. Beets’ ailment, and bids Mudbutter goodbye.