As viewers we may know Pompey’s fate but Caesar is still in hot persuit, and turns up in Egypt, and is, well, lets just say a little upset to discover that what has happened the Former Consol Of Rome! Shame on the egyptians. Shame!
But there is also the fact that Egypt may be on the verge of a civil war, and since Rome needs the Egyptian grain, war is something that Caesar is determined to prevent. So he sends Mark Anthony home with half the legion, while he will stay to arbitrate between Ptolemy and his sister/wife Cleopatra.