Conflict with Cleopatra
In 51 BCE, Ptolemy became the co-ruler of Egypt with his sister until he exiled her from Alexandria. As pharaoh, Ptolemy became a pawn of the Order of the Ancients, who aided him in his war against his exiled sister.
In 48 BCE, Ptolemy learned of the arrival of the Roman general Pompey, who had accepted Cleopatra's proposal for an alliance. In response, the young Pharaoh sent Lucius Septimius and his Gabiniani to eliminate the general. Pompey was decapitated and his head was brought to Ptolemy who hoped to use it as a gift to Julius Caesar in hopes of gaining his favor.
When Caesar arrived in Alexandria in 47 BCE, their meeting was interrupted by the arrival of Cleopatra and her followers Apollodorus, the Medjay Bayek of Siwa, and his wife, Aya. Cleopatra proved to be more successful with Caesar, gaining his favor and becoming his lover, leading Ptolemy to wage war against them both. Led by Achillas and Ganymedes, Ptolemy XIII's armies attacked Alexandria, trapping Caesar's army there. Caesar, however, was able to break through with the help of Bayek and the arrival of his fleet.
Battle of the Nile and death
During the Battle of the Nile in 47 BCE, Ptolemy's regent Pothinus and soldiers were defeated by the efforts of Julius Caesar, Bayek, and Aya. As Ptolemy attempted to escape on a raft with a soldier by his side, he saw Aya, who decided to lower her bow. He nodded at her, but she merely watched as the boy king's raft was ambushed by crocodiles and he died in their jaws.
Personality and characteristics
Being a very young Pharaoh, Ptolemy XIII was a very weak-willed and manipulable ruler, who was more interested in holding the illusion of power than ruling his kingdom. This lust for power, combined with his docile nature, was the main reason for the Order of the Ancients to side with him and make him the Pharaoh of Egypt in the first place. Ptolemy XIII was very ignorant of his role as a puppet ruler, as well as the suffering the Order had caused in Egypt, for which the common people, including Bayek and Aya, hated him.
Ptolemy XIII's incompetence and hot temper proved to be his undoing when he sent Lucius Septimus to kill Pompey and thus appeal to Caesar, which failed, given Caesar's favorable attitude towards Pompey. Seeing how Cleopatra was able to impress Caesar with her charisma and the offer of marriage, Ptolemy XIII became furious and threatened he'd kill all Romans in Alexandria, if Caesar aligned himself with his sister. The two merely dismissed him as insignificant, and this caused him to run away, showing his lack of personal strength and courage as a Pharaoh. Faced with defeat and the loss of his kingdom, he attempted to flee from the battlefield, only to be intercepted by Aya, and crocodiles.