Queen regnant and regent
Cleopatra Selene's location during the reign of Antiochus X's successors in Antioch is unknown. She evidently took shelter with her children somewhere in the kingdom, and possibly fled to Cilicia or Coele-Syria, probably the city of Ptolemais, which she held until her death. Antiochus XII, another son of Antiochus VIII who was ruling in Damascus, died in 230 SE (83/82 BC). With the throne of Antiochus XII vacant, Cleopatra Selene declared her son Antiochus XIII king.
Based on the evidence of the coins depicting her alongside her ruling son, it appears that Cleopatra Selene acted as the regent. Many of those coins have been found, and they depict Antiochus XIII in the background and herself in the foreground, in the style of a queen regnant, where Cleopatra Selene's name is written before that of the king's. When she declared her son king, Cleopatra Selene controlled lands in Cilicia or Phoenicia or both. The archaeologist Alfred Bellinger suggested that she was in control of several coastal Syrian cities from a base in Cilicia; she certainly controlled Ptolemais and probably Seleucia Pieria. The 1st-century historian Josephus wrote of "Selene ... who ruled in Syria", indicating her continued influence despite her never controlling the capital Antioch. Her children probably remained in Cilicia or somewhere else in Asia Minor for protection, which would explain Antiochus XIII's nickname, "Asiaticus".
According to Josephus, "those that held Damascus" invited Aretas III, King of the Nabataeans, to rule them because they feared Ptolemy (son of Mennaeus), king of the Iturea. Damascus' history between the death of Antiochus XII and 241 SE (72/71 BC), when the Armenian king Tigranes II took the city, is obscure. Based on her jugate coins which depict her alongside Antiochus XIII, Hoover suggested that Selene operated from Damascus; those coins used a broken-bar Alpha, cursive Epsilon and squared Sigma. This typography appeared in the Damascene coins of Demetrius III and Antiochus XII and is otherwise rare in the Hellenistic world. If her currency was minted in Damascus, then it dates to the period between the death of Antiochus XII and Tigranes II's occupation of the city. Two scenarios are possible:
Cleopatra Selene took Damascus after Antiochus XII's death and was replaced by Aretas III before 73 BC: Josephus does not name the people of Damascus as the party who invited Aretas III, rather, his words indicate that a garrison or a governor conducted the act. All known coins of Cleopatra Selene are made of bronze, and the absence of silver coinage indicates that the queen lacked the necessary resources to defend Damascus, which would explain the invitation of Aretas III. It is also possible that Cleopatra Selene moved her capital to Ptolemais, causing her troops in Damascus to lose faith in her rule, leading them to invite the Nabataean king.
Aretas III's rule in Damascus did not last long before Cleopatra Selene took control: Wright suggested that Cleopatra Selene's takeover of Damascus took place after 80 BC. Several factors might have compelled the Nabataeans to withdraw, such as the Ituraean threats or the attacks of the Hasmonean Judaean king Alexander Jannaeus, whose incursions into Nabataean lands must have made their position in Damascus difficult.
In the north, Philip I ruled until his death, after which Cleopatra Selene claimed the rights of her children with Antiochus X to the vacant throne. The queen's claims of authority were not generally accepted by the Syrians, and the people of Antioch invited Tigranes II to rule Syria, being frustrated by the Seleucids' constant civil wars. The year in which this event took place is debated; 83 BC is, without any proof, commonly accepted as Philip I's year of death by the majority of scholars who count on the account of Appian, who assigned a reign of fourteen years for Tigranes II in Syria, which ended in 69 BC. Oliver D. Hoover suggested that Tigranes II invaded Syria only in 74 BC, with Philip I ruling until 75 BC in Northern Syria, allowing Cleopatra Selene and Antiochus XIII to claim the country unopposed for a while. An argument in favour of Cleopatra Selene and her son being the sole claimants of Syria in 75 BC is a statement by Cicero: the Roman statesman wrote that Antiochus XIII and his brother were sent to Rome by their mother in 75 BC. The brothers went to petition the Roman Senate for their right to the throne of Egypt based on their mother's birthright. To impress the Senate, the queen endowed her children with sufficient assets, which included a jewelled candelabrum that was dedicated to the temple of Jupiter Capitolinus. The Senate refused to hear their petition for the Egyptian throne, but, according to Cicero, their de jure right to the Syrian throne, which they had inherited from their ancestors, was already acknowledged. Antiochus and his brother returned to Syria in 240 SE (73/72 BC).
The statement of Cicero indicates that in 75 BC, Tigranes II was still not in control of Syria, for if he were, Antiochus XIII would have asked the Roman Senate for support to regain Syria, since Tigranes II was the son-in-law of Rome's enemy, Mithridates VI of Pontus. Likewise, Philip I could not have been alive since Antiochus XIII went to Rome without having to assert his right to Syria. In a paper presented at the 131st annual meeting of the American Historical Association, Nikolaus Overtoom, based on Hoover's chronology, suggested that Cleopatra Selene was in control of the south while Philip I ruled the north until 75 BC; his death meant that Cleopatra Selene's son was the strongest candidate to the throne, but Philip I's faction, being opposed to Cleopatra Selene, offered the crown to Tigranes II who invaded and conquered the country in 74 BC.