The following assumes that all information revealed during ME2 is true and isn't misunderstanding or misinterpreting facts.
1. Reapers are in fact governed by a host of AI at the same time.
Each is a nation, with many, potentially millions or more AI processes running at a single time. This is revealed by Legion during dialogue.
2. Reaper AIs inhabit portions of the Reaper as need determines. (Speculation)
When the Reaper IFF begins broadcasting the Normandy's location this is an indication of a reasoned, malevolent force inhabiting the IFF. There are no normal conceivable reasons to build in such a failsafe into a device used to identify friends and foes.
One logical conclussion is that one of the derelict Reaper's AI processes had inhabited the IFF as a Geth inhabits a mobile platform. Upon reaching the Normandy and assessing its situation it determined the best possible means of rescue was to reconfigure its own systems or those of the Normandy to signal for rescue.
3. Cerberus through some front organization managed to retrieve vital components from the wreckage of Sovereign that it used in the creation of the Normandy SR-2 (Fact) Among these components was one or more Reaper AIs or remnant code patterns from Sovereign. (Speculation)
4. EDI begins the game as a shackled and extremely controlled AI, only used by Cerberus to attempt to fight the Reapers. Cerberus is only using the technology to put them on an equal footing with the Reapers in cyberwarfare.
5. Cerberus has a long history of using unethical means including enslaved or repurposed lifeforms for their own ends. See: Husks, Rachni, Thresher Maws, Biotics.
6. EDI is a Quantum Blue Box AI. Her intelligence being housed in that technology. Codex entries stress: "Without its blue box, an AI is no more than data files. Loading
these files into a new blue box will create a new personality, as
variations in the quantum hardware and runtime results create
unpredictable variations."
So, just a supposition, a speculation, a wild guess. Lemme know how crazy I sound now.





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