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The Battle of the Nile was a skirmish involving the Roman-Egyptian forces of Julius Caesar and his recent lover Cleopatra against the Ptolemaic forces of her brother Ptolemy XIII, backed by the Order of the Ancients.
After pursuing his rival Pompey to Egypt, Caesar became entwined in the Alexandrine Civil War after his rival was killed by Lucius Septimius on Ptolemy XIII's orders, in an attempt to please Caesar. When Pompey's decapitated head was presented to Caesar, he was anything but impressed.
The Roman legions destroyed a Ptolemaic fort, and after heavy fighting stormed Ptolemy's camp. Thousands fled, including Ptolemy, who drowned when his boat was attacked by crocodiles and capsized. Although Aya was tasked with killing Ptolemy, she saw he was trying to flee and left him to be eaten. Bayek hunted down the eunuch Pothinus and killed him and his war elephant. After Caesar informed Bayek of Lucius Septimius' whereabouts, Bayek went to find him.
Bayek defeated Septimius, but was prohibited from killing him by Caesar, who claimed that because Septimius was Roman, he would be dealt with under Roman law. The Roman soldiers had to psychically restrain a furious Bayek from attacking Septimius further. Egypt was now in the hands of Caesar, who placed Cleopatra on the throne.
After Caesar defeated Ptolemy's army and installed Cleopatra as ruler, he fathered his only known biological son with her, Ptolemy XV Caesar, better known as "Caesarion". Septimius was spared from execution while Bayek and Aya were removed from Cleopatra's services shortly after her coronation.