The Galaxy is built on a cycle of extinction. For an undetermined length of time, possibly since the beginning of it all, a struggle has gone on between organisms, and machines. The Reapers , apex of evolution and existence, the most powerful beings in the known universe, harvest us for reasons beyond our understanding. Every 50,000 years, a civilization rises to its zenith and is destroyed. Nobody knows why. At first it was believed the Reapers did this so they can harvest our genetic material to substitute for Reaper reproduction, but this is not so. Reapers leave behind a vanguard, if that vanguard fails, they create a new one, the real reason probably equates to something having to do with metaphysical essences. A theory is believed to exist that says the Reapers are actually metaphysical beings trapped inside metallic shells, literally a spirit inside a machine. Perhaps the Reapers' technology and nature blurred forming a second nature, they became so dependent on technology that they became it, and over many millions of billions of years they became something else, so far along the path of a new evolution, they cheated death, lived for so long they could not remember what they once were, they could not fathom ever once being mortal, or ever having a beginning, so they could not even begin to imagine having an end. In order for their metaphysical energies to survive and live, they must prey on the energies of others, and this requires the energy of an entire galaxy. This is only theory, however. The battle came to its highest point, when organics had the best chance to defeat the Reapers in 50,000 years. Every 50,000 years, the forces of the Milky Way come closer to defeating the Reapers. The Prothean race came the closest, now, a decade until the 23rd century, the civilizations of the Galaxy have a fighting chance.
The short but bloody conflict known as The Eden Prime War, is a series of battles named after its place of origin, a human colony once known as Eden Prime where an attack instigated by a rogue council spectre by the name ofSaren, led to an intergalactic battle with the arch-nemesis of the Quarian people known as the Geth. This led to the induction of Commander Shepard into the spectres to pursue Saren. The conflict took place over a period of time slightly longer in length to the First Contact War, only more lives were lost. Saren and his flagship Sovereign were the two most powerful forces during the conflict. Shepard's search for Saren took him to Feros, Therum, Vimire,Noveria, and finally a capitol of the ancient Prothean empire, Ilos. Over the course of his investigation, Shepard learned that this wasn't about humanity fighting for survival, but it was about all races of the Galaxy, and that this wasn't Saren trying to destroy humanity, but the fate of all Galactic civilizations was at stake.
Shepard learned that the Citadel was in actuality a single massive relay which led to dark space, a location where the sentient machines, known as Reapers lie dormant, those responsible for the demise of the Protheans, and all of those before them. Shepard battled against Saren and several of his henchmen, eventually even battling a powerful asari matriarch, Benezia. However, the most startling discovered he makes, is that Sovereign is actually not a ship at all, but a Reaper vanguard left behind to activate the Citadel relay. Shepard and his team then managed to track Saren back to the Citadel through a backdoor known as "The Conduit". Saren has now almost been completely indoctrinated, but Saren eventually overcomes the indoctrination, and kills himself. Shepard finally faces off against Sovereign controlling Saren's Avatar. When the Systems Alliance Arcturus Fleet arrives and saves the Council, Shepard destroys The Avatar, momentarily stunning Sovereign, allowing Alliance Ships, including Shepard's ship, the Normandy, and Ambrose's, the Pegasus, to deal the killing blow to Sovereign once and for all. The Reaper threat has momentarily been stalled, but not for long, as a few months later, a new threat surfaces, known as The Collectors.
Two years later, 2185, Shepard, who was among the KIA list of the SSV Normandy, is reanimated by the black ops division of the Alliance gone rogue, known as Cerberus. This does not change Shepard's grudge against Cerberus for the deaths of his unit on Akuze, in fact, it makes him even more angry, the fact that they would not even consider his feelings towards them. It just made them seem all the more soulless. Nevertheless, Shepard reunites a majority of his original crew, with a lot of new faces, and manages to build up the loyalty of his team. Shepard manages to acquire a Reaper IFF, Geth Technology, and discovers the Collectors, the ones behind the attacks on Human colonies, are in fact re-purposed Protheans for use as husks by the Reapers. They also discover upon entering the Omega 4 relay and boarding the Collector Base, which just so happened to lie at the galactic core, that they were building a new Reaper to replace Sovereign. Shepard thwarts their plans, and Illusive Man's by destroyed the Reaper and the base, however, the only person to make it out alive, is helmsman Joker. Shepard's death caused a stir in the Galactic community, realizing the Spectres were not as coughed up to what they were expected to be, their rights were greatly restricted by the new council in 2189, and the new government of Omega, the Barony's, partnership with the new Council only caused a greater stir in the galactic community, as did the new Human Councilor, Zikan Drakon, and his overall spiteful attitude. Many however, fell before the Council onto their knees, only one stood against them, Captain of the SSV Pegasus, Ambrose, a friend of Shepard in his youth.
February 5, 2190: First sightings of Indoctrinated forces are recorded on outer rim colonies.
February 27, 2190: More human colonies disappear.
April 3, 2190: Colonies of other species begin to disappear further and further into the traverse.
April 16, 2190: Systems Alliance military forces make first contact with Indoctrinated forces on the battlefield.
June 20, 2190: More colonies attacked deeper into the galaxy, Council species colonies put on full alert.
August 21, 2190: After more colonies fall, the Alliance convinces the Council that the Reaper threat is real.
December 30, 2190: A pattern is found in the attacks. Several spectre led STG forces investigate the next colonies in line. They arrive too late.
January 12, 2191: Ambrose's squad is sent to investigate the Turian Colony of Faunus, however, instead of arriving late, they arrive in time for the attack.
March 22, 2191: Ambrose is put on probation for failing to get his unit out alive.
July 2, 2191: After over three months of nobody doing anything, and learning of his father's presence on the human colony of Rising, Ambrose decides to risk his position as a Spectre and travel to Rising against the Council's wishes. Ambrose locates who he believes to be his father, saves most of the colony, along with his team takes out two of three Council agents, one of them secretly working for Cerberus, one of the three escapes, and he is officially declared rogue by the Council, mainly with use of propaganda.
July 3, 2191: The Illusive Man is killed by a mod instigated by Yarik Streydus and Donnie Cazador, who they accused of handing over information about Cerberus over to the Alliance.
July 4-August 28, 2191: Ambrose spends his time upgrading the Pegasus from all the races in the terminus and recruiting the deadliest warriors from across the galaxy and tracking the Indoctrinated threat through all their incursions in the Terminus Systems, and backtracking to all the colonies already hit as well, eventually tracking them to an area beyond the Far Rim, on the very edge of the Galaxy, known as Limbo. While on these missions, due to their mistreatment of many of the races without a seat on the council, the Citadel Council and the Alliance get into a heated confrontation, which eventually ends up with the Alliance, and many of the races loyal to them, splitting from the Council forces, while many humans, most of them secret Cerberus agents working for Drakon, stay with the Council, a lot of which were promised by Drakon he would help them overthrow the Council, and assert humanity as the dominant species at the Citadel, while the Alliance is less concerned with politics and 'overthrowing' anything other than the Reapers, and more concerned with making peace between the other races in the galaxy.