Prequel.
Mass Effect: Dawn of the Cycle
It's set 10.7 Billion years ago in the Andromeda galaxy. You're an agent of the second most powerful race in Andromeda, with the original creators of the Reapers being the most technologically advanced at the time. The two of your species have allied to fight against an uprising of fierce A.I. combatants that are an evolved form of Synthetics that seemingly came from nowhere in great force.
Your government has told you that the Bio-Reapers are working on a project to end the war through non-violent means. However, they've been extremely secretive about the operations, and want you and a small team to infiltrate the Bio-Reaper hierarchy to gain access.
After some undercover work, you discover that the epicenter of their war-ending research is in enemy territory on an obscure astral body outside the gravitational field of any star. When you reach the sector, you find out it's really an imitation-moon made out of Eezo with a dark-matter shell. On site the entire construction is a giant generator designed to fuck with space-time and loop a point in the future with the present.
At the heart of all the machinations is a one of the enemy A.I.'s who's actually volunteered to take part in the experiment. Via some interactions with the scientists and the A.I. itself you learn that the experiment loops space-time so that the A.I. and the Bio-Reaper researchers can run practically infinite numbers of simulations to end the war in an extremely short time-span.
The program has already filtered out trillions of possible actions that all lead to the Synthetics completely dominating Andromeda. One of your teammates - who is revealed after the fact as a Synthetic deep-cover operative - manipulates the parameters of the experiment. The next time the volunteer A.I. tries to run a simulation, shit goes down and entire chunks of its data-consciousness are lost to the ever-destabilizing time stream.
In an attempt to preserve the A.I. the Bio-Reapers completely isolate it before you steal it and fight your way out. You catch the undercover Synthetic agent trying to erase the severely damaged A.I., and must decide its fate. It tells you, however, that while the experiment might have found a way to defeat the Synthetics - even without killing them - in the end the very nature of being a Synthetic; the Absolutism inherent in A.I. code as it evolves from the most basic rules created by organics - means that any solution would eventually fall apart as ideologies diverged, even in peacetime.
Your superiors agree, having suspected something similar for centuries. Artificial minds are not built to accept half-truths or partial-benefits. Harmony to an artificial mind takes the form of absolutism by definition, and dissolving the processes so that only majorities of agreements are required - supposedly to give A.I.s the ability to dissent - only fosters evolution of ways to achieve absolutism.
They deem the isolated A.I. (and your companion, if alive) as necessary casualties, having served their purpose, and instruct you to dispose of them. As you begin the process, you catch odd glimpses from what data is viable in the A.I.'s 'brain.' Your companions recognize a few worlds held by your species, you recognize a Bio-Reaper. The record is dated thousands of years prior to the war, but it may be specious due to the quantum experiments performed on the volunteer A.I.
You commandeer the ship, go rogue, and break into your government's and the Bio-Reaper's government's archives and discover the truth: The Bio-Reapers and your species found the Synthetics millenia ago inside a fully operation Dyson Sphere surrounding an artificial star.
It was the repository and monument of a species that died millions of years ago due to biological sabotage on a massive scale during their last war. One of the sides manipulated the genetic code of the species, modifying spans of necessary protein-encoding genes. Benign at first, as the war ended and the species returned to discovering the galaxy, the modified genes mutated - effectively neutering the species over several generations. Due to the passage of time a non-affected piece of genetic code couldn't be found, everything on record was infected. Due to the nature of the manipulation and the specific biology of the species, it could not be removed. They 'revamped' generations as quickly as possible with infected versions that still had some time left before going off, but it was a stall. The population dwindled, and decided they were only cheating their self-imposed genocide. They built the Dyson Sphere and its artificial inhabitants as a way to cement a gift to future species.
However, in an attempt to recreate the artificial star at the heart of the Dyson Sphere, the Bio-Reapers - who had been working with your species - tried to quantum-link it with the original to understand some of its finer mechanics. The original destabilized and went super-nova, and it was thought the Synthetics were obliterated. They survived, spent several millenia planning their revenge, and enacted it centuries before your mission.
On the run from all sides, the crippled A.I. awakens, rambling on about a solution to the war, but unable to articulate it. It tells you its seen a trillion-trillion futures, and it figured out a way for all sides to avoid defeat. It needs access to the quantum-experiment machine again, but reports of select stars building up massive dark-energy cores and going supernova eons before their time indicates the Synthetics have found out how to destroy entire systems.
The Bio-Reapers offer a compromise to the Synthetics; the Bio-Reapers offer to demonstrate an act of good will by partially turning themselves into an artificial being. The Synthetics accept, and quickly start processing the Bio-Reapers into the first "Reaper." One of your companions loses faith in the A.I.'s specious solution, and betrays the crew of your ship to both all sides. The Bio-Reapers pick you up first and bring you in to be processed into a portion of the Reaper at the request of the Synthetics. You successfully hide the damaged A.I. on your person, citing the logs of erasing the A.I. from earlier as proof you destroyed the entity.
Inside the shell of the Reaper itself, you are the first of your crew in line. Unbeknownst to you, a companion turned themselves into a living time-bomb, and sacrifices themselves to save you and the remaining crew. Trapped in the Reaper, you figure the only way out of the situation is to fly the newly minted super-ship the hell out of there.
Making it to the cockpit, you try to fly it, but the ship is somehow resisting your orders as the collective remnants of billions of Bio-Reapers see their chance for peace dwindling away. In a desperate attempt to gain control, you hook the damaged A.I. up to the Reaper, and it quickly forces its way throughout the systems and pilots the ship through planetary defenses.
You reach the quantum-experiment planet, overwhelm its now paltry defenses, and pray the A.I. knows what it's doing. Plugging the suspiciously-capable A.I. into its prior role at the center of the operations, you conduct a final run. In horror you watch as the A.I. runs simulations of a new type of travel method utilizing Eezo, and in the miasmas of the time compression, utilizes the enormous Eezo core of the quantum-experiment world to hurl the lot of you through a massless corridor into the unexplored Milky Way Galaxy.
After your arrival, it apologizes profusely as it knew the war in Andromeda could not be solved. However, it could prevent Andromeda from happening again. As you and your crew take a shuttle to a nearby inhabitable planet, you start to draw up plans for a device that might bring your descendents back to Andromeda. You start with an enormous Eezo core, and record simple "Access" command lines for the damaged A.I. now inhabiting the Reaper hovering over the new world that could potentially be used to query its database should any assistance be required.
The prequel ends with a scene set hundreds of years after your arrival: Billions of your descendents run in terror from the Reaper, the damaged A.I. telling the ruling body that their contributions are necessary if it's to carry out its solution to the problem it was asked to solve. A time-capsule is delivered to a world full of intelligent life, your descendents acting as envoys from the sky with a warning about the "Grand Deceiver" who promises power in exchange for your eternal enslavement.
Roll credits.