In the last 13 years of Ptolemy V's reign he had, by Cleopatra I, the daughter of Antiochus the Great, two sons and a daughter. The elder of the two boys became Ptolemy VI Philometor when he took the crown of Egypt after his father's death. He was still young so his mother acted as regent, but she too soon died, five years later, and two greedy officials took over as the young king's regents. Similar to what had happened to his father, Eulaeus and Lenaeus, a eunuch and a Syrian ex-slave respectively, appointed themselves as his guardians

According to Peter Clayton in Chronicle of the Pharaohs, the two regents foolishly soon declared war on Antiochus IV in 170 BC. However, this situation may not have been so simple. When the Coele-Syria (Sixth Syrian War) broke out around 171 or 170, it is true that Ptolemy VI was no more than sixteen, and still very much in the hands of his advisors. While Diodorus blames the regents for forcing Ptolemy to fight, Livy and others put the responsibility on Antiochus. Others believe that the long history of this territorial quarrel suggest that both sides must, inevitably, share the blame. 

Apparently, in 170 BC, Ptolemy VI declared himself of age, thus obviating the need for a regent. He took the throne name Iwa-en-netjerwy-per Setep-en-Ptah-khepri Ir-maat-en-amun-re, meaning "Heir of the [two] Houses of the Gods, Chosen of Ptah, Truth is the Form of Amun-Re". He married his sister, another Cleopatra (II), and took as their co-regent his younger brother, Ptolemy VIII Euergetes II (Sometimes referred to as Ptolemy VII). 

Irregardless of who initiated the war between Egypt and Antiochus, Antiochus drove south against Ptolemy in the spring of 169 BC, and wiped out the Egyptian expeditionary forces, capturing Pelusium and apparently also his young nephew, Ptolemy VI. Thus, Antiochus became virtual master of Egypt except for Alexandria.

At this point Ptolemy VI made adjustments in his advisors and negotiated with Antiochus who was, after all, his uncle. However, in Alexandria, these events sparked off the Alexandria "Mob". Antiochus's troops had been looting the temples, and so Alexandrians decided to wash their hands of Ptolemy VI, and proclaim Ptolemy VIII Euergetes joint ruler with his sister, Cleopatra. 

Antiochus then apparently made a half hearted attempt to besiege Alexandria, but withdrew in 169. Hence, the two brothers both became, at least nominally, rulers of Egypt. By now, Rome had become a dominating power, and so the Egyptians, on behalf of the younger brother (Ptolemy Euergetes), and Antiochus, who held Ptolemy Philometor appealed to Rome for assistance in deciding the matter. The outcome was that Ptolemy Philometor ruled in the old capital of Memphis, while his younger brother Euergetes ruled in Alexandria with their sister. 

While Antiochus IV returned to Syria in 169 BC, he was still a dominant power in Egypt due to his protection of Ptolemy VI, which was an anathema to the brothers and sister alike. Therefore, they joined forces and appealed to Rome for help against Antiochus. The results were that Antiochus returned to Egypt in 168 BC, marching to Pelusium where he demanded control not only of this frontier fortress, but also of Cyprus, an Egyptian possession. The Ptolemies were not disposed to grant him these concessions, so he next marched on Memphis and then turned north to Alexandria, while his fleet took Cyprus. 

Unfortunately, Rome's hands were tied at this point, because of the country's involvement in the Macedonian war with Perseus. However, on June 22nd, 168 BC, at the battle of Pydna, Perseus was defeated and now Rome turned her attention to the Ptolemaic plea, and sent a three man mission to Alexandria, led by Caius Popilius Laenas. 

The confrontation between the Roman Senate's representatives and Antiochus IV took place in July, just outside of Alexandria at Eleusis. The senate's decree was that Antiochus should vacate Egypt and Cyprus immediately. He asked for time to consider, but Popilius refused. Taking his stick and drawing a circle in the sand around Antiochus' feet, Popilius demanded his answer before he left the circle. Of course, Antiochus realized that Rome was now the major state in the Mediterranean, and he had little option but to comply with the Senate's demands. For a short while the two brothers and their sister all ruled Egypt, but that was not a good situation, and eventually their reconciliation began to fall apart. 

There seems to have continued some amount of of trouble particularly between the two brothers. Though Ptolemy VI showed himself to be a clever, civilized and even an energetic ruler, he apparently became overcome with the machinations of his brother to the point where he went to Rome in 164 BC. He quietly took up residence in a working-class district, in ostentatious poverty, and waited for the authorities to discover his plight and come to him, in embarrassment and with largesse, which they duly did. 

Rome actually did very little, other than to instruct a mission already on its way to Asia Minor to visit Alexandria and effect a reconciliation. Ptolemy VI thereupon took off for Cyprus, to have some sort of base from which to operate. Envoys from Alexandria, where his brother's rule was becoming intolerable, soon arrived begging for his return. This change of heart in Alexandria may well have dictated what happened next. In May 163 BC, the two brothers, with the approval of Rome, agreed on a partition of the Ptolmaic holdings, with Ptolemy VI taking Egypt, and his brother the province of Cyrenaica. This solution, reducing Ptolemy VIII to essentially the status of a crown prince, did not remove the tension between the too brothers for long.

In fact, Ptolemy VIII talked the Roman Senate into backing his claim on Cyprus, though his brother ignored this ruling with the results that Rome sent Ptolemy VI's ambassadors home and repudiated its alliance with him. Ptolemy VI attempted to have his brother assassinated, who then went to Rome to show off the scars from the incident, getting some token military support for his efforts. With five Roman ships and some Roman advisers, along with the authorization to levy Greek troops at his own expense, he attempted to capture Cyprus but that did not work, and instead he was captured by his brother. However, perhaps because he was afraid of Rome's reaction, Ptolemy VI not only allowed his brother to live, but also offered his own daughter, Cleopatra Thea, to his brother in marriage. He also, at Rome's insistence, sent his brother back to Cyrene, preserving the status quo prior to the troubles. Afterwards he sent his son, Eupator, to govern Cyprus, where he died very young in 150 BC.

The Athenians, to whom he had presented a library and perhaps a gymnasium, in gratitude erected a bronze equestrian statue of him on the Acropolis, and celebrated. Benefactions of this kind were common, and formed an integral part of Ptolemy VI's foreign policy, creating not only good will but also, he hoped, a network of accepted obligations. Hence, over the next quarter century, Ptolemy VI's reign passed quietly enough, though things were never exactly quiet under Ptolemaic rule, and Egypt prospered. Ptolemy VI, of course, continued the intrigues that his family were known for to some extent.

Therefore, when a character called Balas claimed to be the son of Antiochus IV got himself mixed up in this adventure. Balas, imposter or not, was sent to Rome where, perhaps for political reasons, the senate approved Balas's dubious credentials. Now while his endorsement may have come from Rome, it was Ptolemy VI and others who were his real backers. At first, Balas, who now styled himself as Alexander Balas, did will in the Seleucid territory. In fat, Ptolemy VI, shrewd and patient, then encouraged him to marry his daughter, Cleopatra Thea, who had briefly been betrothed to his younger brother. Obviously, no Ptolemy would ever pass up the chance to become the power behind the Seleucid throne, particularly while Coele-Syria, an old Egyptian possession, was still potentially recoverable. 

However, Balas seems never to have been anything but a pretender to the throne, and when Demetrius II came to Syria with a force of Cretan mercenaries, Ptolemy marched north, as though to defend his son-in-law.  In reality, Ptolemy saw this as a chance to further his holdings, and Balas, who saw through the guise, tried to procure his assassination. The attempt failed, and Ptolemy pressed on north toward Antioch. His daughter, Cleopatra Thea, found her way back to her father after seeing that Balas was finished, and Ptolemy VI declared her marriage void. coolly prepared to refurbish her as a bride for the young Dmetrius. Of course, the price of such a marriage would be the return of Coele-Syria to Egyptian hands. 

In fact, Ptolemy VI was taken by surprise when the volatile citizens of Antioch decided to acclaim him as their new monarch. It must have been very tempting to Ptolemy VI, to receive the Seleucid monarchy, which had so bedazzled Ptolemy III, but it had come too late. He knew that Rome would probably not be happy with this development, so he refused the offer and persuaded the citizens of Antioch to stick with Demetrius, who promptly became his new son-in-law. Soon afterwards, Balas was killed by an Arab chieftain with whom he had sought refuge in northern Syria after suffering a crushing military defeat, and his head brought to Ptolemy. Unfortunately, in that same battle of 145 BC, Ptolemy himself was wounded, and died two days later. Ptolemy was almost certainly buried in Alexandria, though little of the Royal cemetery remains today. 

The widowed Cleopatra was left in Alexandria with the young heir, Ptolemy VII Neos Philopator, who, for a very short time, was nominally Egypt's king under his mothers doubtful protection. 

As a side note, during his life, Ptolemy VI abandoned a rather old form of portraiture. While his ancestors had portrayed themselves on coinage usually with a modified version of Ptolemy I Sorter's features, Ptolemy VI, on a gold ring bezel now in the Louvre, had himself depicted as thin, almost nervous looking, with a scanty beard. 

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