More than 100.000 years ago, there is highly advanced race which unknown to all Citadel races. Those who know them called them simply, "The Forerunner". Forerunner establishes galactic span empire which encompasses 3 million fertile worlds and constructs many wonder. However, like all civilization, they facing threat that threatens their race continuity.
That threat is the Flood, a parasitic being which originated outside galaxy. Devour anything in touch and assimilate victim body and mind to their own. After 300 years fighting, Forerunner has out of option. They had betrayed by their own intelligence and suddenly, far more ancient structures manipulated by the Flood were ravaging already shattered Forerunner. The last measure was Halo Array, terrifying weapon which capable erasing sentient life nerve within 10.000 light years
Before Halo activated, Forerunner made emergency evacuation to every known sapient life in the galaxy. Many races were saved, but the Forerunner couldn't save their own kind. Finally after all plans were end with failure, Halo was activated, eradicating all life and infestation. Forerunner sends back each races to their own homeworld, starting from begin again. Some species is incapable for recovering and driven to extinction. Forerunner themselves depart from galaxy.
In depth of starless space, ancient sentient starship machine called Reapers which have waiting for opportunity finally awaken. Reaper returns and constructs a structure called mass relay, device that would generate mass free corridor that would travel matter instantly. Mass relay was created from alloy of structure from Forerunner structures; give them incredibly resilient for years and energy.
The center of mass relay network was Citadel, space station which actually dormant enormous mass relay which link directly to Reaper bed on dark space. Waiting for race advanced enough to harvest. The races which discover this would stunt but eventually would stun in development.
On 70.000 BC, Prothean race became spacefaring race by discovering mass relay and discover Citadel and center of their empire. Finally on 48.000 BC, Reaper arrives via Citadel, decapitating Prothean government and their client races, seizing star charts and census data. Prothean fight to their death fiercely.
Those who live under Prothean empire influence are evolved to follow previous path. Those who evolve in this path would form collective alliance based on Citadel which we know today as Citadel Council.
But mass relay can't cover entire galaxy, in depth of space, there is much race live within influence of previous culture, they would create divergent path of evolution which taken by their neighbor. This race was Sangheili and San Shyuum that would clashed and form theocratic alliance know as the Covenant
Humanity, with no access to Forerunner technology have found disturbing discovery that would their existence to near extinction. That discovery was Tiberium which impact on 2015 AD. Development of technology was accelerated, but their existence was pushed. Furthermore, Earth divided to Global Defense Initiative and Brotherhood of Nod. On 2047 AD, humanity in the first time has brutal first contact with alien know as the Scrin. Their invasion was repelled. But Tiberium crisis didn't solved yet, Tiberium evolve unexpectedly and consume 98% globe to unhabitable zone.
On 2077 AD, a solution established, TCN or knows as Tiberium control network was activated, ascending human genetic to next level of evolution as well removing all tiberium from planet surface. Redevelopment was started and human found Prothean data cache in mars on 2148 CE which reveals them interstellar traveling and colonization
On 2157 AD, human for second time encounter alien with brutal contact. Turian caught human activate mass relays and eventually capturing Shanxi. Turian was expelled and prepare for interstellar war. Fortune this time, Citadel Council intervenes before the hostilities escalate further. SDI was incorporated to galactic community and stand as independent and strong.
On 2186 AD, incident occurred on Elysium, third time human contact with other galactic civilization, the Covenant. Fortunately, Covenant instead offers alliance. Massive Tiberium explosion on illium trigger return of the Scrin from hibernation. Nevertheless, Reaper would arrive in months. Commander Shepard of Initiative was ready to fight the worst.