The story of Ar tonelico: Melody of Elemia takes place in the world of Sol Ciel, a world consisting of two floating islands connected by the Tower of Ar tonelico. Long ago people had built up a great civilization under the guidance of the goddesses the Trio of Elemia, but over the years things have changed; there were two disasters that have lead towards the destruction of the world. In the first disaster most of the lands and skies were lost, in the second the super civilization was lost; now in the third era another disaster is beginning. Viruses born in the Altar of Apostles have begun to appear, though normally not in physical form have now taken on the form of monsters and could destroy the world. In the upper levels of the Tower is a city called Platina where the Knights of Elemia reside; their job is to control virus outbreaks to preserve the tower. One such knight is Lyner Barsett; the main character of the story, he will need to go on a quest to find the Hymn Crystal which can save the Tower of Ar tonelico and the whole world.

Ar tonelico: Melody of Elemia is an RPG style game where you control Lyner Barsett. As the game begins, your airship crashes in the lower world; you'll not only need to locate the Hymn Crystal somewhere in the lower world, but then figure out how to return to the upper levels of the tower! Gameplay features both an exploration mode and battle mode. When exploring you can wander around the many locations of Sol Ciel; you'll encounter numerous people to talk to, various towns and cities, as well as locate useful items. In many areas battles are randomly encountered; on the screen is a colored meter - beginning green, it slowly fades towards red. The closer to red the meter becomes, the greater your chances of randomly encountering a battle.

Battles in the game are turn based; Lyner as well as other characters in your party each have the ability to perform attacks as well as utilize various skills. Throughout the game you will encounter several characters known as Reyvateils; Reyvateils have the unique ability to sing songs which can be crafted into powerful magic for attacking, healing, or defense. When a Reyvateil is in your party, she remains at the back during battles; you can give her commands on what songs to sing - the longer she sings, the more powerful the magic will become. However singing tires a Reyvateil, and if she sings for too long she becomes so tired the built up magic is lost so you need to make sure to give a command to activate the magic before that happens. Normally opponents don't attack a Reyvateil, only the characters on the front line. Occasionally though an enemy will target a Reyvateil; when this happens you need to make sure other characters protect her, for though Reyvateils can craft powerful magic they are mostly defenseless to enemy attacks! When all opponents in the battle have been defeated, the battle is won and points are earned which can level up your characters.

Throughout the game you will need to help Reyvateils learn more powerful song magic. To do this you will need to dive into a Reyvateils cosmosphere. The cosmosphere is the world of her mind consisting of her private thoughts and emotions; when there you can interact with the Reyvateil and help her overcome obstacles to learn new songs. However since you are viewing her private thoughts, you first need to gain the trust of the Reyvateil. This is done by interacting in the real world first by talking; talk topics can be found in various locations throughout the world and also after various events. When you have enough talk topics completed you can then dive to the next level in the Reyvateils mind.

Another important skill Lyner learns early on is Grathmelding; this allows you to combine various items to form new ones. To do so, you will first need to locate a recipe so you know what to combine as well as Grathnode crystal to aid the process. The required items can sometimes be bought in shops or may be found by exploring the world. The items you create may be necessary to get past certain obstacles, or can just help you out in battle.

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