After the capitulation of Greece (1941), the Aegean part of Macedonia was partitioned among Bulgaria, Italy and Germany. The Bulgarian occupier endeavoured to attract the Macedonian population by founding companies against the Greek nationalist forces with purpose – the realization of its territorial aspiration over the whole Aegean Macedonia. The Greek factor, both the political left (KPG, EAM, ELAS) and the right wings (EDES, EKKA) endeavoured to maintain the Greek territorial integrity already acquired in 1913 and 1919.
The Macedonian factor, in the circumstances of the fascist occupation, actively participated in the National Liberation and anti-fascist war, with diversity of attitudes: the so-called maximal national programme concerning the union of Macedonia and the so-called minimal national programme concerning the recognition of the Macedonian minority rights in Greece that coincides with the KPG policy. The realization of the maximal national programme was frustrated by KPG and EAM and the Macedonians were permitted only to fight for the realization of the minimal programme within the frames of KPG and EAM – ELAS.
During the War of National Liberation the Macedonians have founded military and political organizations. In 1942 the Macedonian anti-fascist organization (MAO) was founded in Voden District; in 1943 the Slavo-Macedonian National Liberation Front (SNOF) was founded in Kostur (Castoria) and Lerin (Florina) District. At the same time the Macedonian military formations were founded: "Lazo Trpovski" detachment (1943), "Goce" – the battalion of Kostur and Lerin District and the Macedonian battalion of Voden (Edessa) found in June 1944. In 1944 the first Aegean brigade was founded which participated in the final fights for liberation of federal Macedonia.
During the war the Macedonians have succeeded in affirmation of their national and cultural values. The Macedonian newspapers "Sloveno-makedonski glas" ("The Slavo-Macedonian Voice"), "Pobeda" ("Victory"), "Sloboda" ("Liberty") etc. were issued. The first Macedonian schools were opened, the courses for teachers were organized and the primer and the reading book were issued. The Macedonian language was introduced into the religious service. The Macedonian folklore was presented by the Macedonian cultural and artistic groups. The play "The Macedonian Bloody Wedding" was also performed.
In the following years of 1945 the acquirements were again repealed by the Greek government that has continued the traditional policy of denationalization and assimilation of the Macedonian people from the Aegean part of Macedonia.