In the world of Ar Ciel, the Reyvateil region is being threatened by an epidemic that's been killing the citizens. A knight from the Grand Bell, Croix, is sent there to deal with the epidemic. The people of Metafalss, lead by the Grand Bell, rebel against the Goddess who controls the world, in order to achieve their dream and create a utopia by singing a Song in the Hymnos language, called Metafalica - as the legend says.

Melody of Metafalica is an RPG, much like its predecessor, Melody of Elemia, that takes place one and a half years later. It is the second installment in the Ar tonelico series. The turn-based battle sequences from the random enemy encounters are split up into two phases. In the first one, Attack, the different characters can perform various attacks until a time gauge runs out. When there is a Reyvateil in the party, a member of the race who can wield magic by transforming sounds into energy, players can determine which magic to use and the moment to unleash it. In the second phase, Defend, enemies have the opportunity to attack and will target the (up to two) Reyvateil who are singing at the back of the party. The other characters must then defend by timing the defensive moves. The effectiveness of attacks is also often determined by how well the attacks are synced to the requests of the Reyvateil.

The game is largely centered around female heroines and it contains a dive system where Croix can dive into the mind (Cosmospheres) of certain Reyvateils to get to know their feelings and emotions. That game element plays out with text-heavy dating-style elements where the choices can alter the storyline and it is also the system through which new Song Magic is crafted. Diving can only be done to the three main characters in the game and Croix needs to commit to one, it is not possible to hop between them. New "evil" Reyvateil can be converted by using the Dive system and afterwards they will contribute to the party. These are equipped through an additional item slot that affects a character through offensive or defensive means.

Collections with Ar tonelico II: Melody of Metafalica