User blog comment:Suparockr/List of Plotholes throughout the series/@comment-1679409-20120717153223/@comment-91.185.112.253-20120719174701

My personal hypothesis is that Catalyst is a gestalt intelligence made up of every single Reaper mind communicating simultaneously. Thus, it primarily exists within the Reapers, not the Citadel. When an invasion is initiated, Catalyst uploads itself to the Citadel and starts mining for intel and locking down the relay network. The Citadel becomes a hub of communication and supply for the Reapers, as well as a shipyard for new Reapers.

Adams points out that quantum bluebox AIs require huge amounts of power. Even though they can pull energy out of virtually nothing, the Reapers can`t get rid of it in the same manner. An Ai embodying quadrillions of hyperintelligent sapients would require enough power to draw a hell of a lot of attention.

The solution to these issues would be to remote-activate the relay, thus avoiding both premature detection and the energy of the relay screwing up Catalyst`s circuitry. But that`s just my ranting.