The fall of Ali Pasha (January 1822) worked to the detriment of the Greeks and changed the balance of power among the warring parties in both Epirus and west-central Greece and in the other areas. Thousands of armed Ottomans could now head south and be used for the repression of the Revolution. At the same time the Souliotes were blocked and were faced with a choice between capitulation and deserting Epirus or waiting for reinforcements. The second choice presupposed the expansion of the Revolution in Epirus with central Greece functionning as the base of operations. For this purpose, a campaign against Arta was organized, since this was the most important Ottoman military base in the southern regions of Epirus. Apart from the armatoles and the chieftains of the wider region (Varnakiotis, Bakolas, Iskos, Makris, and so on) the majority of the philhellenes who had come to the rebellious areas in the previous months participated in the campaign as well. Led by Alexandros Mavrokordatos, the campaign began in early June with the encampments and the occupation of positions near the fortified town. The crucial battle took place in the region of Peta on 4 July 1822 and was disastrous for the revolutionaries, especially the philhellenes, who were virtually decimated by the Ottoman cavalry. The Ottomans then reached Missolonghi relatively unobstructed but the three-month siege (October 1822-January 1823) was not effective.

The defeat at Peta marked the end of operations in Epirus and the capitulation of the Souliotes, who were forced to desert Epirus. It also marked the emergence of controversies among the revolutionaries. The opposition of Alexandros Mavrokordatos with the most powerful armatole, Georgios Varnakiotis, who soon went over to the Ottomans, is characteristic. In addition, there was discord between the armed men and traditional rivalries revived, such as that between the Souliotes and the other chieftains. Finally, there was also antagonism between the chieftains over the armatolikia, as in the case of Agrafa mountains, which were contested by both Karaiskakis and Giannakis Ragos. All these conflicts of opinion hinted at the decline of the Revolution. The bulk of the most powerful chieftains had moved back to their own regions, others had capitulated while many preserved contact with both the Ottomans and the revolutionaries. Thus, the access of the Ottomans to Missolonghi, the main revolutionary centre of west-central Greece, could now be achieved relatively unimpeded. From the Battle of Peta onwards, the strategy of the revolutionaries and, consequently, the survival of the Revolution in west-central Greece, was centred on Missolonghi. In the summer of 1823 the second siege of Missolonghi took place. The besieged endured the siege until the end of November, when the Ottomans withdrew their forces. However, the death of the most significant chieftain of Souli, Markos Botsaris, in an assault at night was a great loss. At the beginning of 1824 the presence of Byron at Missolonghi contributed considerably to the improvement of the fortification works. In fact, many chieftains rejoined the revolutionaries encouraged by the fact that the Ottoman campaign did not take place that year, and encouraged also by the rumours of the loan administrated by the British philhellenes. Another reason for returning was the opportunity for plunder offered by the subjugated mountainous regions of Arta in the summer of 1824, although these regions were also used by the Greek Revolutionary Administration in civil conflicts carried out in the Peloponnese.