Melody is a spirit who lives inside an enchanted music box, possessing the ability to see people’s deepest and most secret wishes. With her talents, she can make them come true in the dream worlds she conjures.

When Cornelius, a student of the Astral Academy, stumbles upon Melody’s music box and opens it, he unleashes Melody, who decides to create fantastic new dreams for all the Academy's students. Luckily one student is able to escape the curse and summon the Heroes of Trine to set things right.

The heroes must traverse the dreamscapes of the Astral Academy, lush and verdant pirate adventures, face the night on the icy cold tundra, follow a sinister path through a haunted old forest, survive in the surreal world inside the clockwork mind of a mechanical owl, and finally solve all mysteries at the deceivingly cosy homestead of Cornelius Crownsteed.

In addition to the familiar faces of Heroes of Trine, Melody of Mystery reintroduces many fan favorites from Nine Parchments, a Trine universe spin-off story that focused on Astral Academy students. Cornelius is not the only student under Melody's spell - Carabel, Gislan, Rudolfus and Owl are all dreaming of enchanted fantasies.