In the year 2061, a research team managed to create a quantum gateway, a teleportation device using the theory of quantum holes, was successfully used to send a research team to Mars. Throughout 529 years, humanity managed to travel and expand into the universe, conquering and claiming worlds by the dozens.
However, during this time, humanity had unrest. In response, the Earth Empire had created the Armored Command Unit, a machine 40 meters tall that is piloted by a sole human. The ACU has blueprints to make an army, starting from mass and energy, to using them to build factories, and then to units.
In the year 2557, when most of humanity had began to lose faith in the hopes that there was an intelligent alien life force in the rest of the universe, they were wrong. A planet 5 times the size of earth and capable of sustaining life was found.
When the first expedition didn't respond, another was scheduled for another 5 years, but was just added to the lengthening 'investigate hazard; list.
Two years later, a computer AI is successfully implanted into a human brain. The human/AI pair is dubbed a Symbiont. By the year of 2612, The Symbiont program successfully completed its R&D phase, and in 2663, The Third Expansion begins, and The Earth Empire begins to have difficulty managing its colonies. In 2666 Procyon, a Symbiont colony, applied for independence. The Earth Empire sends in troops to maintain order. 3 years later, Militant Symbionts on Procyon attack Imperial troops. Secret 'loyalty' programming installed in all Symbionts is activated. After 9 years, the Symbionts, led by Gustaf Brackman, the inventor of the Symbiont program flee and form the foundations of the Cybran Nation.
In the year 2679, The Earth Empire is contacted by descendants of the Seraphim II expedition, naming themselves the Aeon Illuminate, who claim to have been modified by aliens. The Aeon claim that the— The Earth Empire quarantines the sector and sends Commanders, and after 3 months, contact with all planets bordering Seraphim II is lost. After a grueling 5 months, all contact with EarthCom forces within 10 light years of the Quarantine Zone is lost. By the year 2819, The Earth Empire began to lose control. In addition to fighting both the Cybrans and the Aeon from Seraphim II, Imperial forces are forced to contend with extensive internal conflicts, and the Infinite War begins. In 3256, The old Earth Empire is officially dissolved. The United Earth Federation rises in its place.

Shortly after a young commander is sent to destroy the invading Aeons of the planet Phasic IV, he is cut of from the rest of command. After learning that the Aeon were 4x the number that command gave him, the planet is lost; except for the capitol city: Golden Ages. He and 4 other command units desperately try to defend the city from endless Aeon assaults, but when all hope is lost, they come up with a plan to get the civilians to safety: Send in a commander to destroy the Aeon jammer in order to get the Quantum Gates operational again. After witnessing each of his comrades die, one by one, he is able to get the civilians to safety, but right as he ejects his ACU's pod, it goes nuclear as soon as he enters the Quantum Tunnel, causing it to misfire and send him beyond known space.
This is a story about how a lone human must adapt to overcome a world where peace and harmony are plentiful, and must learn to coincide with the pacifist races of Equestria.


Story gotten from here: http://supcom.wikia.com/wiki/United_Earth_Federation