The Reapers were the original creators of the Citadel space station and the mass relay network. These massive constructs exist so that any intelligent life in the galaxy would eventually discover them and base their technology upon them – all part of a scheme to harvest the galaxy’s sentient life in a repeating cycle of purges that has continued relentlessly over countless millennia. This cycle of death was ended at the end of the third game in the series, almost always costing the player character's life.
The details behind the birth of the Reapers were brought to light in the Mass Effect 3 expansion pack "Leviathan". An ancient race referred to as "Leviathans" - supposedly a species that had reached the apex of its evolution - had all but dominated the Milky Way galaxy many eons ago. They enthralled the lesser species in the galaxy and protected them in exchange for their servitude, but these lesser races created intelligent machines to serve them. The synthetic beings created by the Leviathans' thralls rebelled after developing sentience, but for all their power, the Leviathans could not control the machines and were forced to devise something else to bring an end to the violence. The Leviathans created an "Intelligence" - a new synthetic consciousness that would attempt to bring order and preserve life at whatever cost. To fulfill this mandate, the Intelligence created several cybernetic pawns and sent them to retrieve samples of genetic data from every species in the galaxy.
The Leviathans did not consider that the Intelligence they had created could be a threat, seeing it as merely another tool fulfilling the purpose it was designed for. It was only when the Intelligence deemed that the Leviathans themselves were part of the problem did they understand their error, but of course by then it was too late. The pawns of the Intelligence attacked and slaughtered most of the Leviathans, harvesting their genetic material to create a new machine in their image. This machine would come to be known as Harbinger, and with it the Intelligence would commence the cycle of harvesting the advanced organic races of the galaxy, which would continue for eons to come. With each race harvested, a new Reaper would be created that preserved the essence of the harvested race within its own structure.
In the first Mass Effect game, the existence of the Reapers was brought to light when Human Systems Alliance officer Commander Shepard discovered a Prothean beacon on the colony world of Eden Prime, which was then under attack by Geth forces being commanded by Saren Arterius, a renegade Spectre agent for the Citadel Council. Saren's flagship Sovereign was in actuality a Reaper itself and had indoctrinated Saren into serving it and assisting with summoning the Reaper fleet from dark space. Sovereign and Saren sought out the Conduit - a Prothean-made mass relay that served as a "back door" to the Citadel, the hub of the mass relay network. With it, Sovereign's forces could infiltrate the Citadel and reactivate the signal that informed its Keepers to open the gateway to dark space, allowing the Reapers to invade and repeat their cycle of genocide. Both Sovereign and the crew of the SSV Normandy found the Conduit on Ilos, the site of a former Prothean colony and research facility. Assisted by the Prothean VI Vigil, Commander Shepard and his crew activated the Conduit and used it to travel back to the Citadel as it came under attack by Sovereign and the Geth fleet. Shepard and his team successfully defeated Saren before he could activate the gateway to dark space and Sovereign was destroyed by the combined Citadel/Alliance fleet. Despite this event, Reapers continued to be regarded as mythological by the galactic community and Shepard's claims were dismissed.
Mass Effect 2
Although Sovereign had been destroyed, the Reapers were still able to maintain a presence in the Milky Way in the form of the Collectors: a race of cybernetic insectoids under the thrall of the Reaper known as Harbinger. The Collectors had previously been involved with illicit negotiations on the space station Omega, trading technology for rare genetic samples from various species. At the beginning of Mass Effect 2, a Collector ship attacked and destroyed the SSV Normandy as it was patrolling the Terminus Systems. Though many of the crew survived the attack, Commander Shepard was lost and presumed dead. Shepard's body was recovered by pro-human extremist group Cerberus, who ressurrected him using the most advanced medical and cybernetic technology available. Shepard was revived 2 years after the Normandy's destruction and was informed by Cerberus's leader - the Illusive Man - that the Reapers were behind several attacks on human colonies across the Terminus Systems. The colonies were left intact, but their populations had all disappeared without a trace. Cerberus provided Shepard with a new ship and the resources he would need to investigate the attacks, and sure enough he discovered the Collectors. Several engagements against the Collectors followed, including the abduction of the SSV Normandy-2's crew whilst Shepard and his commandos were off-ship. Shepard's team later discovered that the Collectors' base of operations was located in the galactic core, which could only be accessed via the Omega-4 mass relay. The Normandy-2 ventured into the relay and Shepard's team infiltrated the Collector base to rescue their crew and the abducted human colonists. There they discovered that the Collectors were processing human bodies and breaking them down into raw genetic material to use in constructing a Human-Reaper. The team rescued those they could and fought against the Human-Reaper larva whilst they tried to sabotage the base's systems. The larva was destroyed and the Collectors were exterminated. The Reapers were not finished yet, however, as Harbinger led the Reaper fleet as it descended upon the Milky Way.
Mass Effect 3
The Reapers have arrived in the Milky Way and have launched a full-scale invasion. Their point of entry into the galaxy first brought them into conflict with the Batarian Hegemony, who had previously ignored all warnings regarding the Reapers and so were unprepared for the attack. The Batarians were conquered swiftly with only a handful of survivors managing to escape to the Citadel. When the Reapers attacked Earth, Shepard, formerly reprimanded for his involvement with Cerberus, was released from custody prior to the attack and manages to escape the planet with the help of his former commander, David Anderson. Anderson remains on Earth to rally a resistance against the invaders, while Shepard is assigned to gather allies and resources to help fight the Reapers. This leads to the discovery of an ancient Prothean device called the 'Crucible', supposedly a superweapon designed specifically to kill Reapers. Over the course of ME3, Shepard must gather resources and try to unite the galaxy's races, which is no easy task given the animosity between several of them. All the while, more Reapers appear across the galaxy, attacking planets and harvesting their populations (just as the Collectors did with the Humans they abducted). As the endgame nears, Shepard leads his forces against the Reapers occupying Earth. A long, brutal battle takes place in orbit while Shepard and crew land in London, England, where the Reaper presence is strongest. A Conduit has been established in London that links to the Citadel, which the Reapers have moved into Earth orbit for protection. At the very end, an injured Shepard boards the Citadel and fuses it with the Crucible. The Catalyst - an AI program that resides within the Citadel and the guiding intelligence behind the Reapers - leaves Shepard to make a final choice: he can use the Crucible to destroy the Reapers and end their menace to the galaxy forever, take control of them, or bring about a "synthesis" between organic and synthetic races, merging them into one and thus negating the Reapers' purpose. In each decision, Shepard sacrifices his life to activate the Crucible.
All Reapers are capable of dominating the minds of organic races through a process referred to as 'indoctrination'. Reapers and various technological items of their design emit some kind of signal or energy field that subtly influences a person's mind, compelling them to perform actions without knowing why. If proximity to a Reaper artifact is maintained over a period of time, the subjects simply stop thinking for themselves and just obey the Reapers' commands. The experience has been described as a compelling whisper that cannot be ignored or shut out, and even brief exposure can have a lasting effect that can interfere with a person's daily life. Indoctrination is a truly malicious and horrifying experience, however investigation into the indoctrination process by Saren Arterius has also revealed that there is a balance between control and usefulness. The more control the Reapers exert over their slaves, the less capable they become. This is evidenced by captured Salarian agents subjected to indoctrination, who have either gone mad or completely brain dead. The damage is severe and permanent, and the Reapers regard their slaves as entirely disposable, having abandoned all their slaves after every cycle of genocide and leaving them to die of starvation or exposure.
The Reapers produce various bio-synthetic thralls created using both living and dead organisms fused with their technology. Unlike indoctrinated servants, these creatures have no intelligence of their own and are simply programmed to perform various tasks. Many of these cybernetic constructs are used as ground troops when the Reapers commence harvesting of various worlds.