After his father's murder in 1215 and the succession of his uncle Theodore Komnenos Doukas, he went into exile. According to the hagiography of his later wife, St. Theodora of Arta, Theodore sent him and his mother to exile in the Peloponnese. After Theodore's defeat and capture by Ivan Asen II of Bulgaria at the Battle of Klokotnitsa, the throne in Thessalonica was now occupied by Theodore's brother Manuel Komnenos Doukas, who managed to escape from Klokotnitsa. His domain was reduced to the environs of the city, and his family's core territories in Epirus and Thessaly, as well as Dyrrhachium and Corfu, while his brother Constantine Komnenos Doukas in Aetolia and Acarnania recognized his suzerainty. As a son-in-law of Ivan Asen, Manual was allowed to maintain internal autonomy, but to all intents and purposes he was a client of the Bulgarian tsar. Michael seized the opportunity and returned to Epirus. Michael quickly succeeded, apparently with the support of the local population, in taking over control of the country. Manuel was forced to recognize the "fait accompli" under the pretence that Michael recognized his suzerainty, in token of which Manuel conferred him the title of Despot. In reality Michael was fully independent, and very quickly ceased to acknowledge Manuel's suzerainty; by 1236, he had seized Corfu. Michael II secured the support of local notables by marrying Theodora Petraliphaina, and established a close relationship with the Empire of Nicaea. In 1238, Michael was visited by the Nicaean Patriarch Germanus II and in 1249 he received the court dignity of despotes from Emperor John III Doukas Vatatzes.