The game focuses on the characters Ende and Seres who live in the Elysium kingdom on the continent known as Graecia. Seres is chosen to sing at the kingdom's harvest festival, but monsters begin to attack when she goes to perform. Ende later finds her unconscious as the army comes to take her because she witnessed the beast. A merchant named Graiai helps the two escape into a tower. Later, they find out that Seres has been cursed, and in order to lift it, Ende must use the Orichalcum Chain to obtain the flesh of the beasts that live in the 13 towers. If not, Seres will gradually turn into a beast herself and perish.
The truth of why Ceres was cursed is revealed as you progress through the game. A war broke out 500 years ago between Elusyon and Atenai, two different countries. An unnamed man and woman have a child named Luchil, who they love dearly. In one of the flashbacks Ceres views, for example, when food rations get low they forgo their own meals to feed him.
One day Luchil is playing outside and accidentally drops his toy into a busy street. He runs out into the street after it just as the knights are passing through on their horses, and they trample and kill him in a freak accident. His parents are heartbroken and have difficulty coming to terms with his passing.They pray that the gods will bless them with another child, but it is seemingly to no avail. More than anything, they just want the war to be over so there won't be anymore tragedies like theirs.
What happens next is not entirely clear, but presumably the woman gets caught up in this religious movement/cult-type organization that promises to end the war by unifying the twelve gods using the magic and orichalcum chains of the Dvelg people (like Graiai). The woman offers herself up as a vessel, much to the chagrin of her husband who feels she has left him behind.
As it turns out, the woman will assume as the 6 yin Goddess while her husband will take on the 6 Yang god form. Ultimately, the two of them will merge as one to end the conflict. The elders call off the ceremony partway through because, as they discover, the yin and yang are off balance. In one of the last flashbacks, we see the husband walking away with a baby as the woman calls out to him. Given that the game is all about building a relationship, it is implied that he didn't love her as much as she loved him, and left her for another woman...
There are six possible endings based on your actions and relationship with Ceres herself, mainly, S (The Best Ending), A, B, C, D, and the Bad Ending.