Ok, so I have an idea about the Reapers, perhaps they are an ancient race that downloaded themselves in the bodies of the reapers to preserve themselves or because their bodies were failing them for some reason, much like the Virtual Aliens. They may continue their process of attacking organic life to find an ideal race to renter the world as, which could be humanity. The Reapers seem to have a specific interest in humans, and that could explain why Harbinger wanted Shepard's body intact, perhaps it planned to use Shepard's body as its own.
Response::: I personally have two different theories: 1. The reapers aren't an AI but a VI, part of a system created millions of years ago to prevent overpopulation, over expansion, or over mining of the milky way's limited resources. 2. The reapers were created as highly advanced ships and possibly became sentient and destroyed their creators. The "human reaper" shows that the reapers seem to be using the successive generation to "reproduce." Evidently the reapers are in part biological and it takes millions of creatures to create one. So, to get enough "resources" to produce a reaper, they allow a civilization to develop and spread to gain enough numbers to produce a reaper. The change in shape might be due to how close humanity came to ending the cycle. Evidently the reapers who believed themselves the pinnacle of sentient life discovered they have a weakness and attempted to compensate.
--Another Response: I believe they were an ancient race that developed during a time where they were the only space-faring race (much like Protheons) however it was back towards the beginning of the galaxy so they gained much technological knowledge. They probably abandoned their original forms for some reason (lack of resources or war) for the bio-mechanical forms they now have with several hundred life-forms per unit. However I believe that as time went on their actions they took to survive changed to simply massacring entire species and assimilating them to make more reapers (to replace or to make more I don't know). However it is clear that whatever their origin they are bent on having no one match their level of technology and they need other species.
Um, do I have to announce that this is a response? I honestly don't believe any of the opinions that have been given, as it would be a big disappointment if they were true and Mass Effect 3 told us. I am not saying any of your ideas are bad, I just wouldn't like them. I can't really offer much in the way of my own theory because I can't think of any other theory though. 188.8.131.52 00:13, August 29, 2011 (UTC)