The Turks conquered most of Byzantium's remaining Anatolian territories, and Andronikos spent the last years of his reign fighting his own grandson in the First Palaiologan Civil War.
Made sole emperor by Michael's death in 1282, Andronikos immediately repudiated the union, but was unable to resolve the related schism within the Orthodox clergy until 1310.
The protovestiarios Michael Tarchaneiotes led a force to the town where they were met by the fleet under the command of Alexios Raoul and the megas stratopedarches John Synadenos.
Another marriage alliance attempted to resolve the potential conflict with Serbia in Macedonia, as Andronikos II married off his five-year-old daughter Simonis to King Stefan Milutin in 1298.
In spite of the resolution of problems in Europe, Andronikos II was faced with the collapse of the Byzantine frontier in Asia Minor, despite the successful, but short, governorships of Alexios Philanthropenos and John Tarchaneiotes.
The military victories of Philanthropenos and Tarchaneiotes against the Turks were largely dependent on a considerable contingent of Cretan escapees, or exiles from Venetian-occupied Crete, headed by Hortatzis, whom Michael VIII had repatriated to Byzantium through a treaty agreement with the Venetians ratified in 1277.
[4] Andronikos II had resettled those Cretans in the region of Meander river, the southeastern Asia Minor frontier of Byzantium with the Turks.
Being more ruthless and savage than the enemy they intended to subdue, they quarreled with Michael IX and eventually turned on their Byzantine employers after the murder of Roger de Flor in 1305.
Prusa fell to the Ottoman Turks in 1326, and by the end of Andronikos II's reign much of Bithynia was in the hands of Osman I and his son and heir Orhan.
The conflict precipitated Bulgarian involvement, and Michael Asen III of Bulgaria attempted to capture Andronikos II under the guise of sending him military support.
Andronikos sent an army there in 1298, though its inability to fight a "guerrilla war" made the Emperor sign a peace with Serbia in the following year, sending his five-year-old daughter Simonis as a bride to Stefan Milutin.
Andronikos frequently toured Anatolia to raise the population's morale and restored many fortresses there, yet this could not stem the massive flows of refugees coming into the empire's European holdings.
The Cretans would never be heard of again—though John VI mentions a mysterious village in Thrace said to have been settled by an "army from Crete" before he arrived on the political scene in 1320.
However he faced opposition from the large landowners of Anatolia who his policies were principally aimed against as well as the Church who condemned him for being a supporter of the deposed Patriarch Arsenios.
The enmity faced by Tarchaneiotes boiled over when a small number of Pronoia soldiers laid accusations of rebellion against John before the anti-Arsenite bishop of Philadelphia.
In 1303, the situation in Anatolia worsened to a point that Andronikos considered the most drastic of reforms that being to take all the lands from churches, monasteries, single monks and the imperial entourage and assign it to soldiers.
This would have created more soldiers with more reasons not to desert, and even though there was no notable opposition to this plan the decrepit imperial administration in Anatolia and the ever worsening population flight prevented this from ever being realized.
[8] The economic destitution which plagued the reign of Andronikos II caused him to undertake drastic measures to cut state spending.
As shown by the failed campaign of Andronikos's co-emperor Michael IX, these inexperienced militiamen made countering the Turkish advance a difficult and dangerous undertaking.
For a time the Byzantine navy was completely disbanded, leaving the empire reliant on Genoese and Venetian forces who charged exorbitantly for their service.
Many discharged Byzantine sailors and shipbuilders found employment with the Turkomans, who had just reached the western Anatolian coast and sought to build up their own naval forces.
The resulting new fleets contributed greatly to the exploding problem of Turkic piracy in the Aegean Sea, ravaging trade routes and coastal lands alike.
[9] In 1320, as a result of heightened taxation and more rigorous policies of collection, Andronikos II was able to raise a total of 1 million Hyperpyra for the budgetary year of 1321.
To try and mend this schism, Gregory called for a church synod to which he invited both the Patriarchs of Alexandria and Antioch, asking them to rescind their previous pro-unionist declaration.
The new Patriarch was intensely ascetic, and spent much of his time repudiating clergymen for their earthly possessions; eventually he sought to confiscate property from some of the wealthier churches and monasteries.
When in the summer of 1293 Andronikos returned from a visit to his swiftly-dwindling Anatolian holdings, he was met by a delegation of leading clergyman who demanded the deposition of Athanasius.
Meanwhile, Athanasius personally penned a church bull in which he excommunicated the clergymen who had denounced him, hiding it in a pillar in the northern gallery of Hagia Sophia.