Characters from Persona 3 and 4 have been given a complete visual overhaul to match the Etrian style and plunged into an alternate world resembling Yasogami High School. Legend has it that listening to the end of the bell chimes of Yasogami High's clock tower causes people to die, and this time the bell tolls for the Investigation Team and the SEES. Trapped in an other-world filled with Shadows, the protagonists from Persona 3 and Persona 4 each have different events to follow, allowing the player to choose and experience two different plotlines. As both groups seek a way out of the labyrinth, they will run in to two new characters, Rei and Zen, who may hold the secret to this new mystery.

Persona Q: Shadow of the Labyrinth marks the first time the Persona franchise will be available on a Nintendo system.