He resisted several attempts by Byzantine armies to conquer Thessaly, and allied himself with Palaiologos' Latin enemies, including the Duchy of Athens and Charles of Anjou.

Both George Pachymeres and Marino Sanudo Torcello report that during the march, John became incensed at some Achaean knights, who openly coveted his beautiful wife.

Matters were made worse when William of Villehardouin not only did not punish his men, but also insulted John Doukas for his illegitimate birth, prompting the latter to defect before the battle, after receiving assurances that he would not have to fight his own father; thereupon the Epirotes too left, and the Latin troops were overwhelmed by the Nicaeans.

Nicaean control over Epirus had not yet been consolidated, and father and son were quickly able to recapture the Epirote capital of Arta and then relieve the besieged city of Ioannina.

Michael VIII Palaiologos' gains were rapidly reversed and his rivals quickly regained their strength, with both the Epirotes and Manfred of Sicily reclaiming most of the territories they had lost.

[12] When Michael II died c. 1268, his realm was divided, with Nikephoros receiving the metropolitan territories of Epirus proper and John taking over the Epirote domains in Thessaly and Central Greece.

[14] Nevertheless, John fiercely guarded his independence, and was prepared to ally himself with Latin powers hostile to Palaiologos, namely Charles of Anjou and the Duchy of Athens.

His stronghold of Neopatras was uncomfortably close to the Latin-occupied parts of Greece, particularly the Duchy of Athens and Thebes with which he was in alliance; and it was easier for troublemakers and refugees from [Constantinople] to make their escape to Thessaly than to Epirus".

A commercial treaty was concluded, allowing the export of silk from Thessaly to Apulia and the import of horses from Italy, but it is clear that these contacts were also the first steps for John joining the coalition being prepared by Charles against Constantinople and its ruler.

[18] Michael VIII sought to counter the threat of a new crusade, led by Charles of Anjou and aiming at the restoration of the Latin Empire, by negotiating a union of the Roman Catholic and Eastern Orthodox churches.

Michael VIII would continue to press Gregory's successors, Innocent V and Nicholas III, for the same, as well as for a dissolution of John's alliance with Charles, but without success.

[24] In April 1277, papal legates arrived at Constantinople and forced Michael VIII, his son and heir Andronikos, and the Patriarch John XI Bekkos, to publicly reaffirm their allegiance to the Union at a synod in the Palace of Blachernae.

John once more rejected Michael VIII's overtures for an acceptance of the Union, and on 1 May 1277, convoked a synod of his own at Neopatras which anathematized the Emperor, the Patriarch, and the Pope as heretics.

John convoked another synod at Neopatras in December 1277, where an anti-Unionist council of eight bishops, a few abbots, and one hundred monks, again anathematized Emperor, Patriarch and Pope.

[29] With the threat of an Angevin invasion having subsided following the Sicilian Vespers, his successor, Andronikos II Palaiologos (r. 1282–1328), was quick to repudiated the hated Union of the Churches.

[33][34] After his death, his widow was compelled to recognize the suzerainty of Andronikos II Palaiologos to safeguard the position of her underage sons Constantine and Theodore.