[3] He appears again in 1258, when he participated in the coup launched by his elder brother Michael Palaiologos, then megas konostaulos, against the regent for the underage John IV Laskaris (r. 1258–1261), George Mouzalon.
[5][6] After his coronation as co-emperor in early 1259, Michael raised his brother further to the rank of sebastokrator (Strategopoulos succeeded him as megas domestikos), and arranged a marriage to a daughter of the general Constantine Tornikes [es].
[8] Michael of Epirus, however, marshalled his forces, and was reinforced with men from the Principality of Achaea and the Latin states of southern Greece under Prince William II of Villehardouin himself, as well as a Sicilian contingent.
[11][12] At Lampsacus, John met with his brother, who rewarded his victories with the title of despotes, the second after the emperor himself in the Byzantine hierarchy, while his father-in-law Tornikes and his half-brother Constantine were raised to sebastokratores.
He had estates in the valley of the river Strymon in Macedonia, and is attested in documents concerning the properties of monasteries in eastern Thessaly, which the Byzantines had probably recovered by that time, following the death of Michael II of Epirus in 1267/1268.
[17][18] John Doukas of Thessaly, however, remained one of the Empire's chief opponents, and Michael Palaiologos organized a campaign (variously dated to 1272/1273 or 1274/1275) to finally subdue him.
[19] The campaign was initially crowned with success, as the Byzantine army advanced quickly through Thessaly and besieged John Doukas at his capital Neopatras.
[20] With his forces scattered, John Palaiologos retreated to the north; on his way, he learned of an attack by the Latin fleet on the Byzantine navy at Demetrias.
According to the Byzantine sources, he resigned his title of despotes (although some modern historians have postulated that it was revoked by his brother), and appears to have died shortly after (1273/1274 or 1274/1275, depending on the dating of the Thessalian campaign).