Considering these things can shape shift into whatever they want and hide in plain sight, I find it a little hard to believe that we killed them all.
For all we know there's one laying low in the Tower as a desk lamp or a pulse rifle or whatever, how would we know for sure?
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I really want us to encounter a cool Ahamkara. Like Paarthurnax from Skyrim. Imagine a living, non-taken Ahamkara who actually wanted to aid us. That would be one badass ally in the fight against the Darkness.