Cruxis angels are half-elves evolved by special Exspheres called Cruxis Crystals. The Desians, an antagonist organization primarily consisting of half-elves, are also part of Cruxis. The entire organization is masterminded by Mithos, hero of the Ancient Kharlan War. Serving under his surname, Yggdrasill, Mithos used Cruxis Crystals to transform himself and his allies into angels. Then, using the Eternal Sword, a gift to him from Origin, the King of Summon Spirits, he split the world into two, bipolar parts: Sylvarant and Tethe'alla. This was part of an attempt to resurrect his dead sister, Martel, whose soul was sustained only by using a Cruxis Crystal to bind it to the Great Seed. The Seed had once been the Giant Kharlan Tree, source of all mana, but the Kharlan War caused it to wither and die.
If Martel awakens, the Great Seed will be absorbed into her and disappear. The reverse also holds true. In order to prevent that from happening, Yggdrasill protects the Great Seed with the seals of the Summon Spirits by creating four Mana Links in order to prevent the Great Seed from germinating. . By controlling the flourishing and declining cycle upon Sylvarant and Tethe'alla, Cruxis seeks to prevent evolution of magitechnology upon the the worlds and, more importantly, to create the necessary conditions of a vessel for the revival of Martel. Noticing Mithos' evil deeds, an underground resistance dedicated to fighting Cruxis and the Desians known as the Renegades strive to halt the organizations' objectives
Due to the instability of mana between the two worlds, one world flourishes while the other declines. Every so often, a Chosen One of the mana lineage is born. The Chosen sets upon a Journey of Regeneration, and will become a true angel at the Tower of Salvation, the symbol of the world regeneration. This serves two purposes: to reverse the mana flow of the worlds and find a host body for Martel. Mithos also strives to eliminate discrimination against half-elves in the two worlds. Through the power of Exspheres, he hopes to eliminate the different bloods that flow within elves and humans, thus turning every person in the world in the same lifeless beings. He does not care that millions have to be sacrificed to achieve this, as the only thing that matters is that everyone becomes the same, thus they can not discriminate against each other for being different. For this to happen, he set up the Desians, who mass-produce Expheres in their Human Ranches.
The leaders of Cruxis are the Four Seraphim, composed of Mithos and his former companions. Their base is set on Derris-Kharlan, a great planet of mana and home world of the elves. It is situated directly above Sylvarant and Tethe'alla, but has remained hidden for millennia due to the protective barrier projected from the Tower of Salvation. The only route to Derris-Kharlan is through the Tower of Salvation, which appears in the flourishing world and the declining world at the beginning of the Journey of Regeneration. Angels primarily reside in the holy city, Welgaia. Mithos himself takes residence in his private castle, Vinheim.
The following is a list of the Four Seraphim:
- Mithos Yggdrasill - The leader and founder of Cruxis, as well as Mithos the Hero from the Ancient Kharlan War over 4,000 years ago. Upon his sister’s death, he founded Cruxis and became its leader under his surname, Yggdrasill.
- Kratos Aurion - Mithos' human teacher. Kratos joined him in his efforts to stop the war. After Martel's death, he was forced to join Cruxis. As the only human in the organization, he often goes against Mithos' goals, and once betrayed them.
- Yuan Ka-Fai - A half-elf former companion of Mithos and Martel’s fiance. He secretly formed an underground resistance group called the Renegades.
- Martel Yggdrasill - Mithos' older sister. Martel was killed by a human during the war, but nonetheless, remains the fourth member. She is one of the primary motives for Mithos' actions throughout the story.
The following is a list of various other members of Cruxis:
- Remiel - One of the countless angel minions serving Yggdrasill. Remiel guides the current Chosen, Colette Brunel, on her journey during the story.
- Zelos Wilder - The Chosen of Tethe'alla. Zelos wants nothing more than a normal life. He is unable to have this due to his title, so he eventually joins Cruxis on the condition that his younger half-sister, Seles, becomes the Chosen instead.
- Desians - The pawn organization of Cruxis. They wreak havoc in the dying world in order to create Exspheres and have the Chosen become an angel faster.
- Cruxis is named after the constellation Crux, and Crux is Latin for cross.