STURMANDERUNG. The great explosion.
In 2032 the criminal Syndicate, led by the madman Muro Hasegawa, sabotaged the atmospheric processors of an already ecologically unstable Earth. TCTF agent Konoko was able to destroy the sabotaged processors and prevent them from distributing their toxins; however, the lack of processing allowed the viral agents manufactured in the Biowars to expand beyond their containment. The World Coalition Government rounded up what citizens they could and placed them in biodomes while the TCTF sent teams of robots led by SLDs to examine the outside environment.
However, the Syndicate was not broken by Muro's death; it began to secretly distribute the Daodan Chrysalis genetic augmentation. Individuals with the Chrysalis could survive in the wastes, and the Syndicate used these agents to begin reclaiming overgrown cities and towns. The SLD task forces sent by the TCTF found themselves overwhelmed by the opposition; the WCG soon realized that the Syndicate had effectively imprisioned them and were conquering the planet at their leisure.
Help came from an unexpected source: Bionics and Genetics Incorporated. A medical company that dealt with the Syndicate prior to and during Muro's control, they had access to a number of illegal files regarding Syndicate experiments including the Daodan Chrysalis. In 2057 Agent Konoko convinced the coorperation to surrender peacefully to the TCTF, and their sentence was reduced in exchange for this information. The WCG licensed use of Daodan technology by TCTF agents. This, unfortunately, would begin the Daodan war.
Raging until 2087, the war would claim millions of victims on both sides. In the end, only twelve biodomes remained, at which point both the WCG and the Syndicate realized that pure humans were now a precious resource. A peace treaty was accorded between the two groups, merging them into the Human Alliance, with the TCTF becoming the basis of the new Alliance Military. Research began into lunar and martian colonization, and within seven years new biodomes were placed on the alien surfaces in order to oversee terraforming projects, supported by massive sublight cruisers.
A terraforming expedition sent to the martian south pole in 2148 discovered ancient ruins of alien origin. Descending quickly on the find, the Alliance Military began silent research into every detail of the superstructure and the data contained within. In 2149, element zero drives were perfected and mass retrofitting of the space fleet began; a number of the now FTL capable ships discovered a Mass Relay in Charon, Pluto's moon. Effort was quickly made to unearth and activate it, as the Alliance was desperate to plant new colonies and speed growth of the pure human population; their efforts were rewarded with the discovery of Eden Prime on the relay's other side, and a massive colony was subsequently founded.
With this accomplishment, the Human Alliance renamed itself the Systems Alliance, ad Daodan and SLD citizens had become as much a part of life as the pure human population. Their continued expansion and colonization seemed to be a blessed and wonderful era, unmarred by war and fear. Then, in 2157, this all came crashing down on their head; they opened a relay to an alien fleet, which fired apparently without provocation and attempted to occupy the Shanxi colony. However, while their starship power was enough to overwhelm the scouting ships, their ground forces could not stand against the Daodan and SLD supersoldiers; soon enough, the primary Alliance warships arrived and destroyed the alien ships, capturing the ground troops as prisoners of war.
Shortly thereafter, the Systems Alliance made contact with the Citadel Council, a conglomerate of alien nations that nominally ruled over the galaxy. In exchange for their prisoners, the Citadel ordered the Turians-the race that had attacked the newcomers-to make reparations toward the Alliance; full out galactic war was avoided as a result, although the Turians held some resentment toward the Alliance for their forced reparations. The Citadel Council began to examine the human race for possible integration, but were shocked to find Simulated Life Dolls and Daodan being granted full citizenship; the manufacture of synthetics or sapient AIs in their space was illegal, and the Daodan Chrysalis was considered an extreme form of bioaugmentation by their scientists and inherently unstable.
Nevertheless, the Alliance made it clear that they intended to continue colonization (although they agreed to respect Council territory boundaries) and, upon further research into the development and construction of SLDs, the council was content to classify them as tank-grown humans. In order to keep an eye on this developing power, the Council granted the Systems Alliance an embassy in 2168. The Batarians, disgusted with the seeming favoritism, removed themselves from the Citadel; their crime rings and piracy were ironically compared by humans to the Syndicate of pre-space times.
Since that time, the Alliance has made major economic and diplomatic contributions to the galaxy. Some view them as being too ambitious or desperate to save their founding race, but others see them as rising from a tragedy that only the Krogan can compare to. Still, no matter the public opinion, one thing is certain: The Alliance is here to stay.
-"Systems Alliance: A Historical Overview." Galactic Codex circa 2180.