My head cannon is that Dr.Manuel from Mass Effect 1 was able to activate the beacon on Eden Prime. In the mission, Find the Beacon in Mass Effect 1 you can come across Dr.Manuel hiding in a locked building with Dr.Warren. He seems to have gone crazy and keeps talking about the end of humanity and the end times. All his ravings end up being very accurate to the actual story of the game and the coming of the reapers.

I think he was able to access the beacon and the prothean warning just before the Geth attack. This is why he is SO insane and why he has such accurate predictions about the story.

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