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During World War I Balabán joined the Czechoslovak Legions in Russia. Later, he served as an artillery officer in the Czechoslovakian Army, then as a staff officer and at the Ministry of Defense (reaching the rank of lieutenant-colonel). After Germany occupied the remainder of Czech lands in March 1939, Balabán started to cooperate with the resistance group Obrana národa (Defense of the nation) that had been organized by former army officers. Beginning in the summer of 1939 he was one of the leaders of the organization. Together with Josef Mašín and Václav Morávek, Balabán was part of the group known as the Three Kings (Tři králové), which carried out intelligence gathering and sabotage.
The group continued in communication with Paul Thümmel (agent A-54), a Nazi intelligence officer also working as a spy for Czechoslovakia. The most visible acts of sabotage were two bomb attacks carried out in Berlin: one in January 1941 against the Ministry of Air Travel (Reichsluftfahrtministerium) and police headquarters, and the second in February 1941 in the Berlin-Anhalt rail station, which was intended to kill Heinrich Himmler.
On 22 April 1941 the Gestapo captured Balabán in Prague after a brief gunfight. In spite of being tortured he didn't disclose any information about the resistance. After Reinhard Heydrich assumed the position of Deputy Reichsprotektor (September 1941), martial law was established and Balabán was sentenced to death. He was executed in Ruzyně Prison on 3 October.
Petr Koura: Podplukovník Josef Balabán. Život a smrt velitele legendární odbojové skupiny „Tři králové“ (Lieutenant-colonel Josef Balabán. Life and death of the leader of the legendary resistance group "Three Kings"), Prague, 2003, ISBN 80-86182-72-X.