The player controls Tempo, a Harmoknight in training. Players must hit and jump as Tempo travels through automatic scrolling levels. The goal of each level is to collect as many notes as possible by either hitting enemies or Percussiplants. Players can charge up Tempo's staff to gain a extra note if the next hit is successful. Occasionally, the player will have to control Lyra, who can shoot enemies from a distance with her harp, or Tyko and Cymbi, who will pound all enemies in their way. A few levels will take place on a mine cart that will constantly change the tempo of the music. Boss levels have the player repeating a sequence of actions to the beat.
At the end of every level, the player receives a rating based on how well they performed. If the player wins a good or a great, they receive a Royal Note. Royal Notes can then deactivate Noizoid road blocks that hide more levels. Another bonus is that if the player gains a great, they have the option to play the level at a faster beat. Getting a great on fast mode unlocks concept art.
The game takes place on planet Melodia, the land of music. One day, a huge meteor crash lands on Melodia. From within the meteor, the Noizoids emerge. Lead by Gargan, the Noizoids attack the planet, plotting to fill the world with terrible noises. A boy named Tempo, discovers a magical music note staff that has the ability to dispel bad noises. Tempo's instructor, Master Woodwin, instructs Tempo and his friend, Tappy, to head off to Symphony City. There, Tempo can give the staff to the princess of Melodia, Aralia, who will then give it to a Harmoknight that can fight off the Noizoids.
After meeting the warrior Lyra and the adventurous duo, Tyko and Cymbi, they finally reach Symphony City. Unfortunately, Gargan kidnaps Aralia and puts all the citizens of Symphony City under a eternal sleeping spell. Only Aralia's singing could save them. Tempo and friends chase after Gargan. After a long chase, the heroes find Gargan's hideout at the Baroque Volcano. Gargan then reveals that he is turning the princess into a Noizoid. With Aralia as a Noizoid, he could have unlimited power. Tempo fights off Gargan, sending him into the volcano's center. The volcano then erupts violently, sending Gargan and his Noizoid army back into outer space. Tempo and his friends return to Symphony City. With Melodia safe, Tempo is finally recognized as a true Harmoknight.