We later learn that the beacons were warnings from the protheans about the coming of the reapers, but of course saren already knew about the reapers Saren arterius discovers that humans conduct ai research which has been strictly forbidden since the awakening of the geth Indoctrination is a slow process, but by the comments from various characters in me1, it seems like it's not that slow
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As i recall, the tholian hostage describes it as taking days, even weeks be.
In me saren used it to close the gates in order to stop reinforcements
Shepard opened the relay again to allow the alliance fleet to join the fight So there doesn’t seem to be any need to go into the relays themselves (the most plausible reason why not, in my opinion) the relays are described as cold objects.
