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I like the theory though I, unsure it all ties so neatly together. Are you sure the Borg control systems wouldn't pick up on odd behavior from drones? Or that they're malfunctioning?

No, but the control systems would have to fail if enough drones are infected. If the pathogen itself was designed by something as technologically advanced as Q, and let's all just admit that he has some neat toys but his claims of Godhood are probably lacking veracity. It might even be able to avoid even Borg detection for long enough as it would no longer matter by the time they realized it.