The Reapers are a race of synthetic life that appear every 50,000 years and wipe out every sentient organic race in the Galaxy. Their origins are highly mysterious, known as the "Old Machines" to the Geth, whilst dubbed "Reapers" by the Protheans. Billions of years ago, The Leviathans were the apex of life. The Leviathans noticed that creating synthetics would start a war. The Leviathans created the Catalyst to preserve life. Later, it betrayed them and used the Leviathans' form on the Reapers. The first Reaper was Harbinger. The methods and reasons for the Reapers actions are not understood. It is not clear why the Reapers want to destroy organic life when they return, but they do it because they are programmed to do it viciously and without remorse. Reapers and Reaper technology also have the ability to indoctrinate organic life and corrupt their minds to sway them to the Reaper cause. Indoctrinated agents will even believe what they are doing to be the correct answer to the Reaper problem. To date only two named Reapers' have been met; Sovereign in Mass Effect and Harbinger in Mass Effect 2.
In the original Mass Effect, Commander Shepard first encounters Sovereign on Eden Prime then encounters it again at Virmire and at the final battle on The Citadel. It was thought that the Reapers were a machine race and that they would be comparable to humans and the other organic life in the galaxy in terms of size and stature. The ship Sovereign was also believed to be a space ship of Reaper origin, but those speculations were put to rest when Sovereign introduced itself as a Reaper and stated that its purpose was to serve as a vanguard for the waiting Reaper fleet, that would destroy all life in the galaxy. It is unknown who created the Reapers but they are hyper advanced and are strong enough to decimate any organic life that opposes them. They possess a frightening form of mind control known as "Indoctrination," which allows them to enforce their will on organic beings. The Turian Spectre, Saren Arterius, is an example of one of their indoctrinated agents. It is known that they periodically appear in the galaxy every 50,000 years, when civilization is at its peak. They are the architects of The Citadel, the mass effect fields and relays, thereby granting them complete access to every corner of the galaxy. As individual ships they are extremely powerful individually, with one Reaper able to cause considerable damage to both the Citadel and Alliance fleets.
Mass Effect 2
In Mass Effect 2, the first Reaper known as Harbinger is revealed to be controlling the Collectors, the games' primary antagonists, through the Collector Overseer. Using the Collector Overseer, Harbinger is able to exert direct control over any Collector Drone during combat, massively increasing its strength and defences, to attack Shepard directly.
At the end of Mass Effect 2 it is revealed that thousands of Reapers, including Harbinger, are awaiting outside the boundaries of known space and are preparing to invade the Milky Way.
Mass Effect 3
The Reapers have finally arrived to begin their work to end the current cycle by eliminating all intelligent life that the Reapers have deemed to dangerous and chaotic to keep alive with the less developed life forms of the galaxy. The Reapers began their attack on all organic life by attacking Earth and quickly knocking out major cities and harvesting people to make more husks to attack. The Reapers qucikly spread across the galaxy attacking the other major organic life forms like the, Asari, Turians, and even the synthetic Geth.
The Reapers quickly overwhelmed most of the major civilizations and Commander Shepard is left to pick up the pieces and forge alliances to help bring the galaxy together to defeat the Reapers and finally bring an end to the vicious cycle of the Reapers exterminating life every 50,000 years.