Long ago, the ancient race that composes what Harbinger is built synthetic life. All was good until the synthetics rebelled. During this war, the organics came up with a plan and that plan was to 1)Kill all synthetics and 2) Make sure this problem never happens again. Immediately they figured that order must be imposed and the Mass relay network was exactly how to go about doing that. They figured if they base civilization on a certain technology to begin with, civilizations of the future will develop based on this technology. One by one they built the network and alongside that, members of the organics were volunteering to participate in a project. Harbinger, the first reaper was this project. The machinery to process the organics was made and slowly all the organics "uploaded" themselves to the synthetic organic hybrid known as Harbinger. Once the network and Harbinger were complete, it obliterated all the synthetic lifeforms to ensure that no one else would have to deal with them. In time, other civilizations rose to high levels and as they were extinguished, more and more reapers came to be. The idea behind it was that the only way to prevent other synthetics from dominating organics was to become synthetic themselves. Keep in mind the reapers are basing this on the experiences of the very first civilization that had this issue. They've never experienced what it is like to have organics and synthetics coexist forever. They believe that no matter what, all peace is temporary and that unless it is nipped at the bud, synthetic life will attempt to conquer organics not only because organics are inferior, but because they KNOW organics are inferior. The reapers serve as the salvation, the safe haven, and the method to avoid the fate of complete extinction of all life. Without the reapers, all organic life is doomed and will cease to exist. All these implications in mind, the choices make SLIGHTLY more sense. This DOES NOT excuse how poorly the results were delivered, but the choices in and of themselves DO have potential to go somewhere interesting.

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