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It wasn't long before the new tetrarchs of Judea had to deal with the Parthians who had appeared in Syria in 40 B.C. Pacorus, the prince of Parthia, joined forces with Antigonus in order to seize the throne of Hyrcanus and give it to Antigonus. With the invading of Jerusalem by the Parthians a civil war broke out and fighting went on every day in the city.
When the feast of Pentecost was approaching, and thousands of Jews entering Jerusalem, a Parthian cup bearer named Pacorus arrived bringing word, supposedly, from the Parthian king regarding settlement. The proposal seemed good but Herod became suspicious and did not agree to go meet the king in Galilee, although Phasael and Hyrcanus showed up and they were captured and put in chains. Herod fled to Masada with his troops, relatives, and Mariamne. Later he moved to Petra, the capital of the Nabatean kingdom.
At this time the Parthians were sacking all of Jerusalem and parts of Judea. They made Antigonus king. Antigonus had Hyrcanus mutilated and sent to Parthia so that there would be no possibility of him ever being restored as high priest. Phasael either died in battle, was poisoned, or he committed suicide.
Herod had expected help and protection from the Arabian king Malchus, but he was asked to leave. Herod departed for Egypt and finally made his way to Rome where he was welcomed by Marc Antony and Octavius. Herod told them the whole story and after hearing it they established him as the king of Judea. In 39 B.C. he sailed from Italy back to Ptolemais and marched into Galilee. He captured Joppa and then made his way back to Masada where his relatives were. He found them under attack but with the help of the Roman armies he was able to quietly camp on the west side of Jerusalem.
Herod proclaimed that he was the rightful king and made a promise to forgive all past offenses that were made against him. Antigonus countered by proclaiming that Herod was and Idumaean, and a half Jew, and not a legitimate heir to the throne.
In 38 B.C. Herod overcame any armies in Galilee, and because the progress was slow he requested the help of Marc Antony and the Romans. He divided his army and left part of it with his brother Joseph with orders not to fight until reinforcements came, and with the rest of his army he went to Samosata where Antony was besieging Antiochus, king of Commagene, who had sided with the Parthians. Antony was pleased with Herod's help and his loyalty, and after they defeated and Samosata, Marc Antony ordered Sossius, one of his legates, to use the Roman army in support of King Herod.
King Herod returned to Antioch with two legions and crushed the opposition in Galilee. Unfortunately he also received the bad news that his brother Joseph had been killed at Jericho.
In the spring of 37 B.C. Herod moved his troops to Jerusalem and set up for siege. At that time he left the armies in charge and set off for Samaria to marry Mariamne after about five years of betrothal. By marrying Mariamne he would no doubt strengthen his claim to the throne, even though it was a despicable move against Antigonus.
Once he was married he immediately returned to Jerusalem. Antigonus had been in Jerusalem defending the city against the Roman legions of Sossius, but the city finally fell in the summer of 37 B.C.
When Herod showed up he realized that he needed to stop the Roman armies, who were his allies, from defiling the Temple and plundering the city's great wealth. He went to Sossius and pleaded with him to reward each soldier with a sizable gift. Sossius agreed and called his troops in to reward them and they marched away taking Antigonus to Marc Antony in chains.
According to Josephus Herod had paid a large bribe to persuade the Romans to put Antigonus out of the way. He also records that Antigonus fell beneath the axe. This brought an end to the Hasmonean rule of 129 years. Herod was now the undisputed king of Judea.