There's hardware that's capable of but doesn't always run software that's sufficienty complex to be synthetic life (geth uploading to quarian suits, conversely other geth platforms being described as shells just filled with Reaper code but not actual synthetic life). So it has to somehow distinguish what the software running on a completely alien platform is doing. In other words just try to forget about it, it's another thing chucked in there because the writers wanted something to happen and that thing happening is more important than it making any sense at all. Now of course fiction, especially science fiction is full of things that simply don't make sense or work if you dig hard enough but I expect to need to do at least a little digging before reaching that point, especially on such key, important events.
I've seen stranger things in SF. Ever read the Hyperion Cantos?
Actually, that series' resolution is applicable to ME3, since consciousness itself turns out to be a measurable and, more to the point, alterable phenomenon.





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