Geo Da Sponge said:
That doesn't answer my question. I was asking how they managed to sabotage a system overseen by an ancient, incredibly powerful sentient AI without even noticing the AI is there. I get that they went for the Keepers rather than the AI itself, but you're telling me that the Catalyst had no idea how to fix this, or even what to tell the Reapers? It didn't even think "Well, I can't fix this, better give Sovereign a heads up. Maybe tell him about the Conduit that the Protheans used to invade me".
My guess was that it was in sleep mode, much like the other Reapers in dark space were, waiting for the next cycle and to conserve energy. Face it, even for an AI, 50,000 years is a long time.
Once it woke up from the invasion, and noticed the Crucible being constructed, realized "Oh wait, they might actually pull this off - I'd better move somewhere more defendable." and probably either used the Mass Relay next to it to move, or moved itself since it is a Mass Relay itself and made the technology.
As for the keepers, various mails and such in the game hinted that no one ever really knew how they work. The most the Protheans could do was disrupt the signal for activating the Citadel mass relay, not the basic functionality of the Keepers themselves. And done after they had harvested everyone, so they probably reverted back to their sleep cycle and thus unaware, until the monitor for the galaxy, Sovereign, tried to activate them for this cycle that they realized something was wrong.