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Huna VI had a daughter who married Mar Hanina (the head of the academy) and they had a son, Mar Zutra II. But when Huna VI died without a son, a rival claimant Pachda was appointed to the Exilarchate. A power struggle ensued. In the end it was agreed that Mar Zutra II would marry the daughter of Pachda. When Pachda had no male heir and it became apparent that Mar Zutra II would be the next Exilarch, Pachda resisted. He was removed four years later by King Balash through the exertions of Mar Hanina. In the interval seems the conflict between the Mazdakites and the Jews took on the nature of an armed conflict.

The new exilarch, Mar Zuṭra II, did not obtain the right to autonomous self defense from King Kovad (r488-531 CE). He raised an army including an elite group of four hundred soldiers for the defense of Jewish community. Being denied autonomy, he declared independence. He succeeded in maintaining an independent state for seven years (513-520 CE), collecting revenue even from the non-Jewish population of Iraq. Active measures by the king Kovad put an end, at length, to the Exilarch's state: Mar Zuṭra, only twenty-two years of age, and Mar Hanina were crucified (520) on the bridge of Machoza, his capital; and his infant son, Mar Zuṭra III., was carried to Israel, where founded a new line of Nasiim, Patriarchs. The charge against the Exilarch: misuse of tax money for his person use.

The "Temple tax" collected by the Exilarch was taken over by Kovad, and applied to both Jews and Christians between the ages of 20 and 50, no doubt after Roman example. The Exilarch's army was absorbed into Kovad's army, and were allowed to desist from active operations on the Passover.

Large-scale changes in the pattern of Jewish settlement took place. Many decided to leave Babylonia altogether; and since the Roman Empire was not a safe alternative, the direction of the emigration was at first southward to Arabia and eastward to India and even China