This topic has been discussed in different articles in this wiki. I can cite Arbington’s “ME3 Theories” and, though the issue was debated at some depth there, it wasn’t the main theme of discussion. I’ve looked throughout the blogs and I don’t recall a blog exclusively dedicated to this specific subject. So, let’s have at it.
We can safely say that the galaxy is ill prepared to face an invasion of thousands of Reapers. We witnessed at the end of ME1 how it took the whole Systems Alliance fleet to destroy just one. Shepard later recounts, the names of all the ships lost in the battle. We also witnessed at the end of ME2 how thousands of Reapers awaken in deep space. I don’t want to discuss here the mechanism they will use to come. But one thing is for certain: they are coming.
Obviously Shepard needs to come up with a colossal weapon or weapons of extraordinary power (by galaxy species standards) able to destroy a Reaper with one shot. I think the seeds of such a weapon were introduced in ME2 during the conversations between TIM and Shepard that led to the “Derelict Reaper” mission.
TIM exposes the theory that this weapon was the final act of defiance against the Reapers of a civilization that lived when mammals first started walking the Earth. That’s millions of years. Way before the Protheans and all that came before them.
My theory is that ME3 will return to the ME1 plot progression type of a “Race Against Time” with Shepard searching for clues of this old civilization trying to uncover the technology behind this weapon. Kind of like looking for the Conduit. He/she will fight new Reapers allies/minions in many worlds to find at the end a dormant mass relay which links The Milky Way to another galaxy (Andromeda?). The species inhabiting this new galaxy would have already dealt with, and defeated the Reapers and will teach Shepard how they did it.
This was my theory. Now let’s hear yours.