When Caesar marched on Rome, crossing the Rubicon, Pompey allied with the Senate and fought against Caesar, losing the decisive Battle of Pharsalus (Greece). After the battle, Pompey fled to Alexandria, Egypt, where he was killed by the orders of the young Pharaoh Ptolemy (brother of the famous Cleopatra). Caesar then ruled Rome for a number of years, was assassinated, and the Civil War entered the next phase (Caesar's heirs vs his assassins.)
i thought caesar ruled rome for only a year or so, and was killed soon after proclaiming himself a god.