The main conflict between the United Earth Federation, the Aeon Illuminate, and the Cybran Nation of Supreme Commander, the Infinite War has been waged for over one millenium. It followed the collapse of the Earth Empire after the separation of the symbionts from Earth Command, resulting in the formation of the Cybran Nation, and the formation of the Aeon Illuminate, after the death of the Seraphim on Seraphim II. The Infinite War is fought uniquely using giant Mech-like Armored Command Units, operated by a single highly motivated pilot, that build factories, which in turn create fully robotic engineers and combat units. The Infinite War takes place on various planets in the Milky Way Galaxy. Quantum Gate Networks allow for instantaneous travel between the planets. The Infinite War has claimed billions of lives and has turned planets into nothing more than dead rocks floating in space. The Three Factions have their own problems: the UEF are spread too thin, the Cybrans are outnumbered and outgunned, and the Aeon, while they are close to annihilating the UEF and Cybrans, are experiencing a power struggle.

(Warning, Spoilers!!) The Infinite War came abruptly to an end by the unforseeable emergence of a Seraphim invasion force through a Quantum Rift above the planet Earth formed by Black Sun's firing in October 3844. However, this only marked the beginning of another, even bloodier conflict. This event forced the Cybrans, Aeon, and UEF to forge a hasty alliance against the invaders. However, Brackman's computer, QAI, made with Seraphim technology, rebels and joins the Seraphim, along with a large part of the Aeon Illuminate which renames itself the Order of the Illuminate. The remainder is renamed the Aeon Loyalists, who are loyal to Princess Burke. The Seraphim and their allies are winning this conflict until they are driven back from Griffin IV. The Seraphim warriors are finally stopped when the inter-dimensional arch is destroyed and the Quantum Rift is closed, halting future Seraphim reinforcements. After this, they and their Order compatriots are hunted down, ending the millenia conflict that has ravaged humanity.

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