The story of Melody of Metaflica follows the rookie knight from the Grand Bell Hall, Croix, who is called upon to contain the spreading epidemic called Infel Phira Dependency (IPD). IPD only affects Reyvateils, a race of girls who can use magic by singing songs. The first one we met was Cloche, a bossy princess of the region of Metafalss. Her songs are powerful on their own, but when you eventually meet more of these magical maidens, you can cast song magic with two Reyvateils.

As in the previous game, you have your fighters lined up in front and the Reyvateils in the back. The battle is in phases, in which you take turns with the enemy. During the attack phase, you have a limited amount of time to fight the enemy by pushing corresponding face buttons until the meter runs out. When the enemy attacks, you enter a defend phase in which you need to protect the Reyvateil in your party. A gauge will appear to indicate when you need to hit square to best protect your party member. It's all about timing, and you'll receive feedback (angry feedback from Cloche) if you're not doing it correctly. At the bottom of the screen there is an emotion indicator that shows how the Reyvateil is feeling. Her emotions will affect how the battle will flow and can increase her song magic gauge. A happy Reyvateil is a more powerful one.