In Assassin's Creed Origins, Bayek meets Cleopatra during the main story.
Bayek of Siwa, the game's protagonist, becomes involved in Cleopatra's struggle against her brother Ptolemy XIII. Their alliance gives Bayek access to major political events and helps connect his personal search for revenge with the wider conflict threatening Egypt.
This Cleopatra is Cleopatra VII Philopator, the last active ruler of the Ptolemaic Kingdom of Egypt. She lived from 69 to 30 BCE and ruled alongside members of the Ptolemaic dynasty. Nefertiti and Hatshepsut were also famous Egyptian queens, but they belonged to much earlier periods and are not the queen featured in Origins' central storyline.