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 Roman general Pompey's arrival in Egypt, who had accepted Cleopatra's proposal for an alliance. In response, the young Pharoah sent Lucius Septimius and his Gabinianis to eliminate the general, which they succeeded. 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, their meeting was interrupted by the arrival of Cleopatra and her followers Apollodorus, Bayek and Aya. Cleopatra proved to be more successful, gaining Caesar's favor and becoming his lover, leading Ptolemy to wage war against the both of them. His armies attacked Alexandria, Siege of Alexandria with the forces of his sister and Caesar.
Battle of the Nile and death
As Ptolemy made an attempt at escape on a raft with a soldier by his side, he saw Aya, who decided to lower her bow and spare Ptolemy's life because of her skepticism and grown distrust of Cleopatra's ambitions as well as cruel heart to have order her own brother's death, much to Ptolemy's silent gratitude.
Despite this act of mercy towards the young Pharaoh, Aya could only watch as the young Pharaoh's raft got ambushed by crocodiles and he was killed as a result, leaving Aya feeling disgusted with all she has done for Cleopatra and Julius Caesar.
Being a very young Pharaoh, Ptolemy XII 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, why The Order of the Ancients sided with him and made him Pharaoh of Egypt in the first place. He was very ignorant of his role as a Puppet ruler, as well as the suffering the Order has caused in Egypt, for which the common people hated him.
His incompetence and hot temper proved to be his undoing, when he send Lucius Septimus to kill Pompey and bring his head as an gift to Caesar in hopes to gain his support, which caused the Roman General to hate him. Seeing how Cleopatra was able to impress Caesar with her Charisma and the offer of marriage, he becomes furious and threatened Caesar to kill all Romans in Alexandria, if he would align himself with his sister, only to be dismissed by the two as insignificant and to run away, showing his lack of personal strength and courage as an Pharaoh . Faced with defeat and the loss of his kingdom, he attempted to flee from the battlefield, only to be intercepted by Aya. Her hesitation to kill the young Ptolemy touched by Aya´s compassion, indicating that the pharaoh has a good side in him, despite his role as former puppet ruler of Egypt.