Caesar may have been pleased by the enforced reconciliation he had effected between the two monarchs. But his presence in Egypt and his favoritism toward Cleopatra ultimately produced a war with her brother that literally came to the palace door in Alexandria. The sulky king ran lamenting into the street and tore the diadem from his head to stir up the natural resentment of the Alexandrians against Rome. In this he was helped by his advisors Pothinus and Achillas who felt their influence was receding as Cleopatra's advanced. The Egyptian army, still gathered near Pelusium was turned about and led by Achillas back to Alexandria to put the Romans under siege.

Since Cleopatra and young Ptolemy were still with Caesar in the palace, he could give the uprising the color of a rebellion against the lawful monarchs. But soon, Arsinoe, the younger sister of Cleopatra, escaped with the help of a eunuch named Ganymedes. She placed herself at the head of the resistance and raised the standard of legitimate rule against the puppet monarchs under Roman control. This advantage though was quickly lost when Arsinoe and Achillas began to quarrel. When Pothinus was caught sending messages from within the palace to the Alexandrians, Caesar had him executed.

In the street fighting that was taking place, a fire broke out, perhaps started by the Roman troops to destroy the grain warehouses on the docks. In this fire, a large store of papyri and bookrolls - Livy claims 40,000 volumes - was burnt. It was later rumored and then believed that the famous Library itself had been set on fire by Caesar's carelessness. The spreading of such a story certainly helped blacken Caesar's reputation in Alexandria.

Arsinoe and Achillas continued to quarrel until she finally gained the upper hand and had the army commander arrested and executed, placing the eunuch Ganymedes in charge. He stopped the flow of fresh water from Lake Marcotis into the city and filled the canals and water ways with salt water instead. Lack of water was a serious blow, but Caesar set his men to dig into the harbor beach. With his knowledge of science and topography he had confidence that fresh water would be found there. By morning, they'd reached an adequate spring to hold out.

Severely undermanned, Caesar held out through the winter months until a relief force arrived in early spring. In the early months of 47 BCE the siege continued with no particular advantage on either side. Then a Roman admiral who had brought in the 37th Legion mounted a swift raid on the island and the lighthouse of Pharos and gained control.

The final battle took place near the end of March 47 BCE. By this time, much of the Egyptian fleet had been burned in the Great Harbor (a book depository on the docks also caught fire, prompting the erroneous story that the Great Library of Alexandria had been destroyed), Ptolemy's chief advisors had been killed or fled, and Cleopatra discovered that she was pregnant.

Her defeated brother (now fifteen) drowned in the Nile while trying to escape. Egyptian monarchs were considered divine; to drown in the Nile was a blessed death. To make sure that no stories would arise concerning Ptolemy's resurrection, Caesar had the river dredged until the body was found.

With Egypt secure, Caesar resisted pressures from Rome to annex it as a Roman province. He undoubtedly felt that his personal ambitions were better served by keeping Cleopatra on the throne and by having ready access to Egypt's wealth. Egypt also provided an ideal refuge should he ever need one.

During his remaining time in Egypt, Caesar installed Cleopatra on the throne, married her to her twelve year old brother to conform with Ptolemaic tradition and, in her company, cruised the Nile in style. Cleopatra took him sailing far up the Nile on the Egyptian royal barge, a vessel nearly 100 meters long of unexampled luxury, with audience chambers and private drawing rooms, viewing platforms and canopied sun decks. They would have gone as far south as the Ethopian border had Caesar's army not refused to follow them. The soldiers were desperate for home and Caesar went with them.

When he left at the beginning of summer, Egypt was nominally in the hands of Cleopatra and Ptolemy. But three legions under the freedman Rufinus remained in Egypt with orders to keep a careful watch, 'to support the monarchs', said the Alexandrine War, 'who had neither the affection of their own people, because they had been loyal to Caesar, nor the authority of long usage, because they had ruled jointly for only a few days.' Then the writer added ominously that 'if the rulers of Egypt remained loyal, they would have our protection, but if ungrateful, then these same soldiers would punish them.' And if this warning wasn't sufficient for the Egyptian people, Caesar also took Cleopatra's disgraced sister, Arsinoe, back to Rome with him to walk in chains in his triumph.

Cleopatra's baby was born on June 23 47 BC. The little boy was declared to be the son of a Roman general and named Caesar, though he was always known by the diminutive Caesarion. It was a very provocative act for her to openly proclaim her son in Roman hating Alexandria. But Cleopatra's strength and yet another mark of her intelligent reading of Egyptian history lay in her appeal to the great mass of people beyond the Greek speaking capital of Alexandria.

So the event that enraged Alexandria was celebrated near Thebes. An inscription at Hermonthis welcomed the baby as the child of Amon-Ra created through the human agency of Julius Caesar. The day of birth was declared a feast of Isis, and a coin struck in Cyprus which had just been ceded back to Egypt by Caesar. The coin showed Cleopatra as Isis-Aphrodite suckling Caesarion as the infant god Horus-Eros.

Caesar returned to Rome by the end of July 46 BC after defeating Pharnaces of Pontus and the last of Pompey's followers in North Africa. He held no less than four triumphs to celebrate his conquests in Gaul, Egypt, Pontus and North Africa. Here was a heaven sent opportunity for political show and Caesar made the most of it, particularly the triumph over the colossus of the ancient world, Egypt.

At one moment, the soldiers and underlings of Rome are bawling out ribald songs of the general's amors, of fumblings in oriental courts with a queen of exotic splendor. Then suddenly that queen herself was in Rome, with her brother husband and all her strange retinue. Cleopatra and Ptolemy XIV had come to tie even closer the bond with Rome and to solicit official confirmation of amicitia from the Senate and the people. Caesar was now so completely in control of the Roman state that the recognition was easily granted.

Though they were no longer constant lovers, there was a strong political and human affiliation between Caesar and Cleopatra. Caesar never denied the paternity of the baby who bore his name. Rather he paid Cleopatra as great an honor that was within his power. In the new Forum Julium, contracted by Caesar at huge expense, beside the cult-statue of Venus Genetrix, the goddess celebrated as Mother and Founder of the Julian clan, he placed a gilded statue of Cleopatra.

Some time late in 46 BC, Cleopatra and her court settled into a large villa on Caesar's estate just across the Tiber. Her notoriety, both as Egypt's queen and as the mother of Caesar's son, as well as her strong sense of politics, pulled sober senators again and again to her door. Even Cicero, who could hardly suppress a shudder for the queen, could not keep away. Yet when Cicero came to a final judgment, he could not approve of Cleopatra:

I hate the queen [he wrote in a letter to a friend]. When she lived in the gardens across the Tiber, I cannot speak of her arrogance without pain. I will have nothing to do with these people. They give me no credit for spirit nor even for a capacity of resentment.

Under her influence, leaning on the tradition of scholarship, culture and invention that she brought from Alexandria, Caesar began several plans for improvement and reform. In imitation of the Alexandrian Library, Terentius Varro began the task of bringing together a collection of all Greek and Roman literature. In Alexandria, Caesar had seen the Egyptian-Greek skill in hydraulic engineering, and he now proposed a scheme for a canal that would drain the malarial swamp of the Pontine marshes and link the Tiber to Terracina.

Even more important was the work on the reform of the calendar undertaken on Caesar's orders by the mathematician Sosigenes from the Museum in Alexandria. The lunar year used in Rome had grown seriously out of step with the astronomical year and required a large correction. A new solar year, based on calculations that Sosigenes had drawn from Ptolemaic astronomy, was successfully introduced on January 1, 45 BC. This reform was called the Julian calendar in honor of Caesar. With more justice, it might have been called after Cleopatra and her Alexandrian scientist.

In February 44 BC, at the feast of Lupercalia, Caesar sat in the Capitol on a golden throne and received from Antony the title and diadem of a king. The crowd watched in silence and only broke into a thunder of applause when he took off the diadem and handed it back. There were some things that a true Roman, even a partisan of Caesar, could not stomach, and one of these was a blatant, open assumption of a king's name.

Caesar was set to leave for Parthia on March 17, 44 BC. This war would avenge the defeat and death of Crassus and the loss of the Roman eagles nine years before. Cleopatra also made preparation to leave. Egypt needed her and she needed Egypt.

On the Ides of March, March 15, 44 BC, the swords of the conspirators brought Caesar's dream to an abrupt end.