The Reapers are a race of hyper-advanced machines that existed over 50,000 years ago. There was no record of the Reapers existence until Tali'Zorah nar Rayya gave Commander Shepard a data file she recovered from a Geth's memory core which proved that Saren was trying to bring back the Reapers.
The Geth believe the Reapers to be some sort of God and they follow Saren because he's considered the prophet for the Reapers return. Commander Shepard saw the Reapers in a vision on Eden Prime after he was pulled in by a Prothean Beacon. Shepard could see that the Reapers were the real threat to the Galaxy and not Saren. However, the Citadel Council and Ambassador Udina refused to listen, instead they thought the Reaper's were made up by Saren to distract them. But in actuality, the Leviathans created the Catalyst to prevent synthetic and organic wars. Later, it betrayed them and turned the species into the first Reaper, Harbinger.
 Prothean Genocide
Despite popular belief, the Protheans didn't create the Mass Relays or the Citadel, they just stumbled across them while exploring the Galaxy, much like many races before them. They were actually created by the Reapers as bait for their cycle of galactic extinction. They were created in the hope that other species would develop faster-than-light space travel by themselves, then discover the Mass Relays which would lead them to the Citadel. The Citadel would become the center of galactic civilization for every species that discovered it. The Citadel and the Mass Relays would allow the technology of every species that discovered them to massively advance. Then, once the species of the Galaxy were reaching their peak in technology, the Reapers would appear through a secret Mass Relay behind the Citadel and destroy all traces of the Citadel species.
The Protheans were on the verge of creating their own Mass Relay called the Conduit when they were struck down by the Reapers. First they attacked the Citadel, destroyed the Prothean Government and cut all communications between the Citadel and the Prothean systems. They also gain access to the main data catalogue on the Citadel which had information on every Prothean System and all the Protheans living on each system. In the centuries that followed, the Reapers would travel the Galaxy destroying every Prothean in existence.
 The Vanguard
After destroying the Protheans, the Reapers headed back into dark space where they would remain until the next genocide. One Reaper must stay behind as a Vanguard to assess the evolution of future species and warn the Reapers when it's time for the next attack. After the Protheans were removed, Sovereign was the Reaper that stayed behind. Sovereign stayed hidden in a state of hibernation for 50,000 years while it scouted the events of the Galaxy.
Sovereign was discovered in 2162 by a Batarian Buisinessman and a Human Scientist. When word reached Saren about the discovery of a giant ship he looked into the case himself. He killed the Batarian and the Human and claim the ship as his own. When he finally discovered the true power of Sovereign, he made it his goal to convince the Reaper that the current species of the Galaxy were worth saving. His intentions were good, but the more time he spend aboard Sovereign the more his mind became indoctrinated by the energy field within the ship that could influence his mind. Saren was completely unaware that the Reapers were controlling him and still believed that what he was doing was for the good of the Galaxy. His status as a Spectre made him a powerful puppet for the Reapers. He was able to bring the Geth out of the Perseus Veil and into Citadel Space without detection to attack Eden Prime.