In the final years of Akhenaten, Smenkhkare was leading a bogus rebellion in Palestine/Israel with the purpose of undermining Akhenaten's rivals. Smenkhkare was technically in disgrace, although rebellion was part of his mandated mission based on typecasting.
Nefertiti was probably still alive in the final three years. She seems to have survived Akhenaten's fall from power and fulfilled her role as "Miriam" in the Exodus narrative.
Queen Tiye was clearly the family "Hathor" and acted as the destructive "Queen/Goddess of the Exodus" ala Hathor at the end of the time of the gods. Isis also had a role during the end of the divine age and beginning of the dynastic era.
But, why would Nefertiti need to usurp or copy the throne name of Smenkhkare? Possibly this was an identification of Nefertiti as "the Isis" with Smenkhkare as "the Osiris". She might also have assumed some kind of deified protective role with respect to "the Horus" Tutankhamun. Recall that Horus the Younger was the true son of Hathor and only adopted by Isis as her son. Queen Tiye was the actual mother of Tut.
Isis was also the first female that ruled as a king/man. This may have also motivated Nefertiti.
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