Whilst publicly dedicating himself to rebuilding the ancient city of Letopolis, Taharqa's family knew nothing of his clandestine activities; in fact, his father-in-law, Ghupa, unknowingly agreed to spy against him for Harkhuf, an informant of Apollodorus.
At some point during the 1st century BCE, Taharqa travelled to the Sinai peninsula in pursuit of the Shards from a Star legend, in which a sacred rock was said to have fallen from the sky into Egypt. Taharqa hoped to recover the shards from the rock, intending to honor Amenmesse, a pharaoh of the Nineteenth Dynasty of Egypt, but he ultimately abandoned the search.
- "The Order of Ancients will remember me as the bringer of waters and a builder of cities."
- ―Taharqa's final words to Bayek[src]
In around 48 BCE, shortly before the Medjay Bayek of Siwa came to Sais, Taharqa had Ghupa beaten and tortured, including having his tongue cut out after Ghupa discovered a handsome payment Taharqa had made to a local captain in exchange for his loyalty. A cunning deceiver, Taharqa was able to divert suspicion from himself by finding Ghupa and bringing him home after the soldiers who caught him left him for dead.
In his quest for vengeance against the Order of the Ancients, Bayek was directed to Taharqa in Letopolis by the latter's wife and son in Sais. Unaware of Taharqa's true nature, Bayek visited him and asked for his aid in finding The Scarab. Before he could answer, Taharqa was alerted to a raid by local group of bandits known as the Disciples of the Lioness, who often used the sandstorms that ravaged Letopolis as a cover to plunder the city. In return for his aid, Taharqa promised Bayek answers. After managing to defend the city and slaying the bandits at their hideout, Taharqa invited Bayek to join him and his family for a meal, where Taharqa had promised to discuss The Scarab. However, Taharqa drugged Bayek's drink, and he only realised Taharqa's true identity after noticing his smile and snake-shaped ring just before passing out.
Taharqa had Bayek buried in the nearby desert up to his neck, leaving him for dead and telling the soldiers doing the dirty work to strip him of his gear and have it shipped to Sefetu, Taharqa's ally at Fort Nikiou. After escaping with the help of his horse and Senu and recovering his possessions from a military camp nearby, Bayek returned to Letopolis to exact vengeance, assassinating Taharqa from above as he prayed to the goddess Nut in the Temple of Horus.
As he laid dying, Taharqa was convinced his achievements for the Order and for himself would cement his name through history, and that his name would never be forgotten. Bayek, holding a miniture scarab in his hand that he tossed to the ground, told Taharqa that his creations and achivements would only turn to dust, and his name would truly be forgotten.
After his death, Tarhaqa's son Kawab would attempt to seek vengeance against Bayek, tracking him throughout Egypt and eventually to the Sinai in 38 BCE. Kawab hired two mercenaries to patrol the peninsula to eliminate Bayek, though they were later hunted down themselves. Bayek eventually discovered Kawab's location and defeated him in unarmed combat. Bayek convinced Kawab to give up following Taharqa's footsteps and join Bayek's order, the Hidden Ones, a precursor to the Assassin Brotherhood..