This story contains *spoilers* regarding Mass Effect, Mass Effect 2, and Mass Effect 3.
While a previous familiarity with the Mass Effect universe is not required, it is highly, highly recommended.
Prologue
In the year 2148, explorers on Mars discovered the remains of an ancient spacefaring civilization.
In the decades that followed, these mysterious artifacts revealed startling new technologies, enabling travel to the furthest stars. The basis for this incredible technology was a force that controlled the very fabric of space and time.
They called it the greatest discovery in human history.
The civilizations of the galaxy call it Mass Effect.
Using relays supposedly built by the now-extinct Prothean's, humanity quickly discovered that it was far from being alone in the universe; in fact, the universe was full of a wide variety of sentient species. Humanity's first encounter with such a species left much to be desired.
Having newly discovered the Mass Relay's and curious about a much more accessible galaxy, human explorers travelled far and wide, activating every relay they could find. This occurred without incident until the humans attempted to activate relay 314, an inactive relay that had been forbidden from being used since the Rachni Wars. The Turians, another spacefaring species, witnessed humans attempting to activate the relay and opened fire. This led to a short but bloody war that would be known throughout humanity as the First Contact War.
After the fall of Shanxi, a human colony, the Council stepped in and negotiated peace between the two races. Humanity discovered the Citadel for the first time, an enormous space station built by the Prothean's and home to the Council. Over the course of nearly thirty years, relations between humanity and the Turians would be strained but steadily improving.
Of all of heroes humanity had to offer in the 22nd century, none were more prominent than Commander Shepard. Growing up as a colony kid on Mindoir was hard enough, but then Batarian slavers attacked the colony, killing Shepard's family and friends. One of the few survivors of the Batarian onslaught, Shepard was rescued by an Alliance patrol ship. With no home or family to go back to, Shepard's military career began there.
Surviving against impossible odds is a trait that would come to define Commander Shepard. While investigating a missing colony on Akuze, Shepard and her entire platoon of marines was set upon by Thresher Maws, giant vicious creatures that burrowed through the earth. Fifty marines had landed on Akuze. Only Commander Shepard made it back to the landing pad alive.
Being the sole survivor of the slaughter on Akuze garnered Shepard a lot of attention. That, combined with her stellar career record, placed her as a candidate for the Council's elite team of operatives.
Special Tactics and Reconnaissance. Spectres, everyone called them.
If she passed the test, Shepard would be the first human ever to become an operative of the Spectres, a giant leap forward for a race as young to the Council as humanity was. There was a lot riding on her success from the very beginning.
It was supposed to just be another routine mission; investigate the distress call from Eden Prime while current Turian Spectre Nihlus evaluates Shepard for her potential placement in the order. This does not go according to plan, however; it is discovered upon landing that the colony of Eden Prime is under attack by a race of artificial intelligence called the Geth. Nihlus runs into his former mentor, Saren Arterius, during the investigation. Nihlus let his guard down, and Saren shot him in the back.
Commander Shepard, with the aid of a former C-Sec officer, a Krogan bounty hunter, a Quarian engineer, and Alliance soldiers, chased Saren across the galaxy, discovering along the way something far more sinister; Saren is merely a pawn, a servant of an ancient race of sentient machines known as the Reapers. Sovereign, Saren's flagship, is actually a Reaper left over from 50,000 years ago as a vanguard to usher in a new Reaper invasion. If Saren and Sovereign succeed, all civilized life in the universe will be wiped out, just as it has every 50,000 years previously…
As it turned out, the Citadel was the key; the Citadel was in fact a dormant Mass Relay designed by the Reapers to be the gateway into the galaxy. Saren, finally realizing he was an indoctrinated servant of Sovereign, took his own life. Sovereign attempted to activate the Citadel relay, but through the efforts of Commander Shepard, the Alliance, and Council fleets, Sovereign was destroyed.
It was a battle that came at great cost. To save the Council, many human Alliance ships were destroyed by Sovereign. However, the valiant actions of humanity during the crisis resulted in the Alliance receiving a seat on the Council. Shepard knew the real threat was still out there, even if no one wanted to listen; the Reapers were still coming.
Then, the unthinkable happened.
While out investigating reports of Geth sightings, the SSV Normandy was set upon by an unknown force. The Normandy, outmatched and outgunned, was torn apart. Shepard, in order to save Joker – the Normandy's helmsman – was lost.
Commander Shepard had died.
But, it was not to be the end. Deciding that she was too important to lose, the human splinter group known as Cerberus spent a fortune rebuilding Shepard and the Normandy. The Illusive Man, the head of Cerberus, had only one request; investigate the disappearance of human colonies in the Traverse systems.
Shepard's investigation led her to discover that the Collectors were behind the abductions, an insectoid race many believed to be only a myth. But, just like Saren before them, the Collectors were only the servants of the true threat; the Reapers.
Shepard put together the best team that she could, consisting of many different races with many different backgrounds, and led them through the unmapped Omega-4 relay to take the fight to the Collectors. It was a suicide mission to the heart of the galaxy, but everyone knew what they had signed on for. Once there, Shepard learned a terrible truth; the abducted colonists were being liquidized and used to build a humanoid Reaper! Shepard and her team were able to defeat the monstrosity, but their troubles were far from over.
In awe of the Reaper technology that the Collectors had access to, the Illusive Man ordered Shepard to save the Collector base so that humanity could take advantage of the technology. Knowing what the technology of Reapers did to people, and unwilling to compromise her morals to advance humanity, Shepard refused, cutting ties with Cerberus and blowing up the Collector base.
It was time to face the music though; the Alliance impounded the Normandy and put Shepard on trial. Though her actions had been in service to the galaxy at large, she had been working with Cerberus, a recognized terrorist cell and avowed enemy of the Council. Held under house arrest in Vancouver, Shepard awaited a verdict that would never come.
Something big was coming, and it was coming fast. Finally, the Alliance decided to listen. Finally, they asked how to stop the Reapers. But it was far too late.
The Reapers had invaded, unleashing terror across Earth. Shepard barely escaped with her life, picked up by Joker and an Alliance retrofitted Normandy. Together, they set out to do the impossible one last time.
Their goal? To unite the races of the galaxy into a united effort against the Reaper threat. Their only hope lay in the hands of a design for an ancient Prothean weapon, the Crucible, supposedly capable of destroying the Reapers.
And do the impossible they did. With Shepard at the helm, they cured the Krogan genophage, ending a millennia of torment. They reconciled the Geth and the Quarians, allowing the space-faring species to finally return to their homeworld. All the while every resource available was going toward building the Crucible, preparing for a final stand. The only thing missing from the schematic was something that was referred to only as The Catalyst, the crucial component that the Prothean's never acquired before the Reapers wiped them out.
But the Reapers were not the only threat. Convinced that Reaper tech was the future of humanity, the Illusive Man outfitted his soldiers with Reaper upgrades. While Shepard sought the means to destroy the Reapers, the Illusive Man believed the answer lay in controlling the Reapers, turning their signals against them and bending them to humanities will. Indoctrinated and obsessed, the Illusive Man waged his own war amidst the Reaper invasion, but it would be his undoing. He would not realize what he had become until the end, but he took comfort in that his last view was of Earth, which he had done such terrible deeds to try and save.
The Catalyst had been revealed, however: it was the Citadel. It seemed only fitting that it would all end where it had began, especially since the Citadel had been moved in to orbit above Earth. Shepard led their combined forces in battle above Earth, fighting down to the streets of London. Shepard fought countless Reaper soldiers, survived an attack by Harbinger, and finally made it to the Citadel.
There, she finally discovered the truth; the Reapers were merely the tool of an ancient artificial intelligence, the true Catalyst, a flawed A.I. who had come to the conclusion that synthetics and organics could never live in harmony. To prevent them from wiping each other out, every 50,000 years the A.I. sent its Reapers to harvest the organics, to forever preserve them as part organic, part synthetic. However, the A.I. tells Shepard that Shepard's presence as the first organic to stand before it means the solution will no longer work. It presents Shepard with the multiple options the Crucible provides; the ability to control the Reapers, the ability to make all organics part synthetic, or the ability to destroy all synthetics (specifically, but not limited to, the Reapers).
Unwilling to go back on her beliefs and control the Reapers, like the Illusive Man had wanted, and unable to force synthesis on every organic being in the galaxy, Shepard chose to destroy the Reapers, even though it would come at great cost. Shepard gave her life to end the war with the Reapers, once and for all.
That was her story. Commander Shepard, savior of the galaxy several times over, gave the ultimate sacrifice. However, this story, the one that has yet to be told, is only just about to unfold. Commander Shepard's tale may be over, but down on the streets of London the story is only just beginning…