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Having attained the episcopate, he devoted himself entirely to confirming the doctrine of the Henoticon, to abrogating the Council of Chalcedon, and to persecuting the orthodox, with the support of Peter the Fuller and his successor Palladius. However, when Flavian II was substituted in place of Palladius in the year 498, and had disappointed the hopes of the Monophysites, Philoxenus began to agitate against him; in the year 499, as it seems, he sought the royal city Constantinople to incite the Emperor Anastasius against the patriarch.
The Persian War, waged in the years 502–505, diverted the emperor's mind a little from dogmatic disputes; but, once matters were settled, Philoxenus traveled to Constantinople again and so moved Anastasius that Flavian was forced to subscribe to the Henoticon again, to anathematize some bishops by name, and to repudiate the Council of Chalcedon; yet these things having been done, he did not in the least appease the hatred of Philoxenus, nor did he have any rest until Flavian, having been ejected from his see, was relegated to Petra in the year 512. Philoxenus and his bishop friends then installed the famous Severus as patriarch of Antioch without delay.
In the year 518, upon the death of Anastasius, Justin I, an orthodox, obtained the empire. In the following year, he expelled most of the bishops who were supporters of the Monophysite doctrine into exile, and among them was Philoxenus. He was first deported to Philippopolis, a city of Thrace, from where he wrote a letter to the Senunense monks in the year 522. Shortly after, he was transferred to Gangra in Paphlagonia, and there he died, suffocated by smoke, in the year 523, at the age of more than eighty years.
That the works of Philoxenus were frequently copied by his Monophysite followers is attested by many codices in which they have reached us, even if not all, at least the greatest parts of them. Attributed to him are: