My take on the back story of the Mass Effect seriesI'll start off by saying that I am a big fan of the Mass Effect series. That being said, I do think that the ending left a lot to be desired. I built this theory around the story that was presented to help resolve some of the issues I had with the series as a whole. (Again this is just my take and is in no way canon.)

We don't know who created the reapers, but we do know that they were created some time hundreds of thousands of years ago. The reapers were synthetics implemented by their creators in an attempt to prevent the death of organic species by the synthetics that they had created. I like to think that the original purpose of the reapers was to keep other synthetics in check,...

My take on the back story of the Mass Effect seriesI'll start off by saying that I am a big fan of the Mass Effect series. That being said, I do think that the ending left a lot to be desired. I built this theory around the story that was presented to help resolve some of the issues I had with the series as a whole. (Again this is just my take and is in no way canon.)

We don't know who created the reapers, but we do know that they were created some time hundreds of thousands of years ago. The reapers were synthetics implemented by their creators in an attempt to prevent the death of organic species by the synthetics that they had created. I like to think that the original purpose of the reapers was to keep other synthetics in check, and should they reach the point of destroying organic life, the reapers would come in and put a stop to it. This worked for a time, but eventually something went wrong. A synthetic revolt occurred, and the reapers were not able to repel the threat before it was too late. Their creators had been destroyed. The reapers decide that the system that they had originally put in place is no longer effective, and decide to find a new way to preserve organics. Thus the harvesting process is decided to be the best way to save organic life. By harvesting organics before they can make the mistake of creating synthetic life that has destructive potential, they preserve organic life forever. Eventually the reaper consensus decides that the Mass Effect relays that their creators had built would serve as the benchmark for whether or not a species would be harvested or not. If an intelligent species had accessed the mass effect relays, they would be harvested, for the relays serve as an unbiased way to decide who had reached their evolutionary peaks. This cycle worked effectively for hundreds of thousands of years. Eventually the reapers harvested the Protheans, bringing the story to Shepard's cycle. This cycle brought something the reapers had never seen before. In all if the previous periods, a single species had dominated, much like the Protheans, in a true show of survival of the fittest evolution. However, in this cycle, they found that many different species had reached the evolutionary stage of harvest. Asari, Turian, Salarian, Quarian, Batarian, Elcor, Hanar, and Rachni (With humans, drell, volus, and others hot on their heels) had all reached this evolutionary precipice, and needed to be preserved. The reapers realized that this group of different species had the potential to repel the reapers, which caused them to do something they had never been forced to do before: Intervene early. The reapers realized that had these races all been left unchecked, they could be a legitimate threat to the harvesting process. The reapers looked to the rachni, a species great in numbers, who were susceptible to indoctrination and capable of great violence, as their solution to this problem. The rachni would ravage the galaxy, and be the only species left for when the reapers came. However they did not count on the krogan, who were forced to ascend their evolutionary cycle in order to defeat the rachni, winning the war and saving the other species. This explains why Harbinger describes the Krogan as "A waste of potential", as they were forced to evolve, and did not grow the way nature intended. However this was only a minor setback as their plan half worked, causing billions across the galaxy to die, thus decreasing their odds of successfully repelling a reaper invasion. This brings us to the beginning of mass effect. Humans have survived the first contact wars and have accessed the mass relays. This forces the reaper hand as they had not planned to harvest humans in this cycle, yet they have accessed the relays. They must move quickly to preserve humans as they are only a few years away from harvest. This brings about the circumstances of Mass Effect 1&2. The reapers are kidnapping human colonies in order to save their genetic line for when the harvest occurs. Eventually Saren is killed, the Collectors are stopped, and the time for invasion is nigh. This brings us to the events of Mass Effect 3. Sovereign decides that they now have enough of each harvestable species to keep their genetic identity alive. They then bring their army forward to battle only to be stopped by a coalition of all of the species in the galaxy. The crucible seems to come out of no where in Mass Effect 3. The way that I reconciled the crucible in my head goes back to those that created the reapers. I think that the reapers were only a temporary solution, and that the crucible was something of their design that would serve the same function the reapers did, only without the potential for the inevitable revolt of synthetics. The crucible could wipe out all synthetic life in the galaxy should it be necessary, thus making their solution of the reapers obsolete. However they were killed by either the reapers or another synthetic before they were able to finish it. Throughout the cycles, this weapon of mass destruction was improved upon, finally able to be finished in Shepard's era. The catalyst is a fail safe. It is an AI, one that was implemented as the last line of defense in order to fire the crucible. When Shepard gets to the Catalyst, it recognizes that it's solution of the reapers is no longer applicable, as the crucible is finished. Shepard then goes on to use the Crucible to destroy synthetic life (I consider the red ending to be the "correct" ending).

Well, that's my take on all of that, if any parts were unclear I'll answer any questions in the comments. Thanks for Reading!