Cruxis is an organization founded by Mithos after the death of Martel. Cruxis are angels that were once half-elves, evolved by special Exspheres called Cruxis Crystals. These Crystals allow the user to lose their human features such as urges to sleep, eat, feel pain, or emotions, unless equipped with a Key Crest. The Desians, a group of primarily half-elves, assist Cruxis in their plans by mass producing Expsheres out of humans in their Human Ranches. Together, with a pact with Origin, they gained the Eternal Sword, which split the world into two bipolar parts: Sylvarant and Tethe'alla. This was in attempt to resurrect Martel, whose soul was only sustained from a Cruxis Crystal in the Great Seed. Mithos also hopes to eliminate the discrimination of half-elves in both worlds by equipping everyone with an Exsphere, eliminating different blood that flows in humans, elves, and half-elves. In the end, everyone would turn into the same life-less being. Mithos loses control and doesn't care that millions of people will have to be sacrificed for this goal (Once again goes along with my Hitler reference).

The leaders of Cruxis are known as the Four Seraphim, or Four Angels. Their base is on Derris-Hkarlan, a great planet of mana and home world of the elves. It is protected by the barrier around the Tower of Salvation, so it remains hidden for a millennia. Mithos Yggdrasill, Kratos Aurion, Yuan Ka-Fai, and Martel Yggrasill are thought to be the main leaders of Cruxis. Remiel, Zelos Wilder, and the Desians are also main players who assist. However, Yuan begins to realize how horrible his actions are, and that he is not fulfilling the main wishes of his beloved, Martel... Yuan ends up betraying his dear friends Mithos and Kratos, and forms his own group, the Renegades.

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