In May 1941, at the beginning of the
Nazi German occupation of Greece, he, along with other Greek military prisoners, escaped from the island of Gavdos and began what was to become the original underground work against the German
occupation, initially in Crete, later in Athens, Thessaloniki and eventually all of
Macedonia. In 1942, he was elected into the
Central Committee of the Communist Party of Greece and was named supervisor of the Macedonia wing of the
Greek People's Liberation Army (ELAS). In May 1944, he was elected as a representative of Thessaloniki to the
national congress that took place at the village of Koryschades in
Evrytania, but was unable to attend. On 30 October 1944, after the withdrawal of the German army, and following battles against the Security Battalions, he entered as liberator in
Thessaloniki with his men of ELAS. In November 1944, his forces liberated
Central Macedonia and helped save thousands of
Greek Jews from imminent peril from the exiting Nazi regime. In February 1946, Markos Vafeiadis disagreed with
Nikos Zachariadis, the general secretary of KKE, who wanted to create a standing communist army. Vafeiadis believed that the forces of the Greek government were too strong, and the best option for the KKE was a guerrilla struggle. However, in July 1946, Zachariadis appointed him as leader of the communist
guerrilla formations. In October 1946, when the General Command of the
Democratic Army of Greece (DSE) was founded, Vafeiadis assumed its leadership, and in December 1947 he was appointed
Prime Minister and
War Minister of the
Provisional Democratic Government. During the last stages of the
Civil War his disagreement with Zachariadis on issues of
military doctrine led to his removal from leadership (August 1948) and later from all offices (January 1949). In October 1950, he was ousted from the Communist Party, while he was in exile in the
Soviet Union, where he had fled after the breakup of the DSE. ==Post-Civil War==