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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Mara Sov has an egg, that we could see in the helm space when you walked through the portal. Also they arrived with the traveler, and given how many places the traveler has been, there are probably Ahemkara all over the universe.