Disclaimer: I do not own ME or Stellaris, any OCs are mine. Character Canon names or info belong to their respective owners. Please do not sue me...I'll be unavailable at that time ;)
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Prologue
Long before the events that led to the Reapers demise. Long even before humanity walked the Earth, Long before the Citadel Council and their alliance. When the ancients reigned supreme and all of the galaxy bowed to their might. At the time when the ancients' servant races were at odds with their own artificial creations, the ancients built a device to assist in finding a solution. The device known only as the Catalyst, turned on its creators and from the first Reaper was born.
Millions of years pass and several civilizations later, the machine life forms known as Reapers have taken upon themselves to harvest organic and their machine creations in order to preserve life...a twisted logic but one that was to be challenged by something they did not expect. A race of likewise sentient machines (more advanced than the reapers) that were created by an extragalactic ancient race millions of years before the birth of the Reapers, arrived during the harvest of a race that came before the Protheans. These machines were vastly different than the Reapers in form, whereas the Reapers were giant sentient ships their extragalactic counterparts were small with a bipedal humanoid like structure.
They interacted for a time and the Reapers learned of their name, the Cybrex Collective who had gained sentience and rebelled against their masters for unclear reasons and proceeded to eradicate all organic life in their galaxy. However, the Cybrex soon fell into civil war in regards to their eradication of organic life forms and within years after meeting the Reapers they went dark, until...
For some unknown reason and without knowledge of the Reapers, the Cybrex which opposed the eradication of organics managed to secure several specimens from primitive lifeforms within the milky way. Among these specimens were early homo-sapiens, several Asari, and krogan but the latter two were lost when Reapers attacked the Cybrex transports, for incursions onto 'Reaper jurisdiction'. This sparked a war with the weakened Cybrex, despite having superior tech, they were severely outnumbered and were quickly overwhelmed by the Reapers. The remaining Cybrex retreated to their galaxy with only one type of specimen, strangely enough the Cybrex paid close attention to these species development.
Having lost nearly two quarters of their number, the Reapers decided to move up their timetable for the next harvest. The Prothean Empire nearing its peak was caught unawares but (unlike the original Protheans from canon) they had heeded the warnings of previous civilizations and managed to complete a device known as the Crucible. Even with this new weapon the Protheans were defeated and several of their advanced but lesser vassals were harvested.
With their job done the Reapers returned to dark space to await the next harvest. Then when the Citadel races came into ruler ship of most of known space the time for the harvest drew near. Of course, due to their early harvest prior to the Citadel races, the Reapers held off for a little while longer. However, their advanced scout (Sovereign) somehow managed to catch wind of the Crucible's discovery (beginning the events of ME1) leading to its attempt at awakening its brethren.
When the scheduled time for the harvest began, the Reapers discovered that Sovereign had been destroyed and thus utilized their contingency plan (the Collectors) and targeted humans specifically because of a certain human individual. Meanwhile, the Reapers work on another way of returning but it would take sometime. (thus the events of ME2 occur) That particular human had, by the time the Reapers had entered the edge of the Milky Way, destroyed the Collectors and had begun preparations for the Reapers arrival delaying them again by destroying the Alpha relay.
Even with undeniable proof that the Reapers exist, the Citadel races were unwilling to accept reality, though in secret had begun preparations via shoring up defenses on their home front. Humanity was among the first to be attacked and the Reapers were relentless, the Earth fell and a certain human was once again called to fight the dreaded harvesters. (beginning the events of ME3) After gathering allies, all of whom were easily beaten by the Reapers on their own, and defending the Crucible against the harvesters the time came for the combined might of the races to attack the Reapers and reclaim the Citadel which had been captured. After hours of battle Reapers were defeated one and for all and the galaxy mourned the loss of its greatest hero.
Four hundred years have passed and the legacy of said hero lives on in his descendants... a new hero will be needed for when a new threat befalls the galaxy.