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Since its creation, the temple has served as a place of worship to the cult of Amun for many generations, with Nitokris, and her daughter, Isidora, serving as the High Priestess and the God's Wife of Amun in the late 1st century BCE.
In 70 BCE, Bayek of Siwa visited the temple with Aya and Tuta, a street urchin he met in Zawty. There, Bayek consulted Nitokris for the whereabouts of his father, Sabu, but was instead directed to his friend, Kensa, who was in the city.
Years later, Nitokris' daughter, Isidora, had succeeded her position as the God's Wife of Amun after her death. In 38 BCE, Bayek, now the Mentor of the Hidden Ones, visited the temple to sought the aid of Isidora regarding the "curse", having being directed by Merti. There, Isidora directed Bayek to visit a village outside the city which still worshipped Akhenaten and Aten.
In 1340, Egyptian Templars fled to the now-decaying Karnak after stealing the Scepter of Aset from the reigning Sultan, Al-Nasir Muhammad. The next year, the Egyptian Assassin Numa Al'Khamsin and his apprentice Ali Al-Ghraib encountered the Templars at the temple complex.
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