Except Traynor figured EDI out in 6 months. Organics that have the technology for space travel and can create AI will notice that the station OS is much more complex than what is required for the station's operation.You both work off the assumption that the catalyst would have to be completely separated from the citadel for to remain hidden. A stance I firmly and strongly disagree with. They can physically observe the keepers (and do, with cameras) and see them interacting with the citadel. How is that more stealthy than having the entire system OS secretly being sentient? How are they going to notice an AI in the system with the system IS THE AI? What kind of sense does it make that something so intelligent couldn't hide its presence? Even EDI could hide it to a degree and she was constantly interacting with the organics on board, drawing attention to herself.
Even assuming it did however why would it build itself with no root admin access? It has no backdoor? It built it but decided to design it in such a way that it itself cannot actually access it but some random reaper vanguard can? It didn't notice that a bunch of protheans changed its body after the cycle was complete? I went into more depth with this particular subject here so that's all I'll say about in here.
More, the Citadel was built by the Reapers. It wouldn't have existed without them and thus can't be the intelligence, since the intelligence created the Reapers.
The intelligence controls the Reapers and, therefore, the vanguard who sends the signal that activates the relay to the dark space. Through the Reapers and the keepers it had full control of the station.





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