Atsız, despite postponement of his punishment, was arrested while he was getting out of the court gate on 9 May 1944.
President İsmet İnönü spoke his speech severely blaming Atsız and his friends and upon this speech, Atsız and his 34 friends were brought to trial in Istanbul Martial Law court in Istanbul. The suspects, among whom there are university professors, teachers, officers, doctors and university students, after being subjected to various tortures under the name of inquiry, were put on trial on 7 September 1944. This trial, called Racism-Turanism Action and which continued for 65 sessions 3 days a week, came to an end on 29 March 1945, and Atsız was sentenced to 6.5 years.
Atsız discerned the decision and Military Court of Appeals quashed the decision of Martial Law Court No. 1 from basis. Thus, Atsız, being kept as a prisoner for one and a half years, was released on 23 October 1945.
The action filed on 5 August 1946 against Atsız and his friends with Martial Law Court No. 2, in which they were not under arrest in the beginning, came to an end on 31 March 1947 and all of the suspects were acquitted after 29 sessions.
Atsız, who was not given a job from April 1947 until July 1949, had to sell some of his books to live on between October 1945 and July 1949 .Atsız, who worked in Türkiye Yayınevi for a period of time, had to publish his book summarizing the Turkish-Russian wars, named Türkiye Asla Boyun Eğmeyecektir (Turkey will never yield) under the name of the person named Sururi Ermete.
When Prof. Tahsin Banguoglu, one of his classmates became the Minister of National Education, appointed Atsız to Suleymaniye Library on 25 July 1949.
Atsız, working in this duty for a period of time, was appointed as the Literature Teacher of Haydarpaşa High School on 21 September 1950 pursuant to the coming to power of Democrat Party.
Upon his conference on Liberation of Turkey, he spoke in Ankara Ataturk High School on 4 May 1952, Cumhuriyet Newspaper told lies against Atsız. The speech of Atsız was found out to be scientific against whom official proceedings were filed by the ministry. However, Atsız was dismissed from his duty as the literature teacher in Haydarpaşa High School on 13 May 1952 with the provision of temporarily and was appointed to his duty in Suleymaniye Library.
This library happened to be the place of longest official post of Atsız, who worked in Suleymaniye Library as from 31 May 1952 until 1 April 1969 when he retired.
He worked as the editor of weekly Orkun magazine published between 1950 and 1952. He undertook the general chairman duty of Turkists Association initiated in 1962. He published Ötüken magazine from 1964 until his death.
The term President Cevdet Sunay, replied the remark the administrators give soil to the Arabs, but they do not to us, Turks by a worker on his way to Gaziantep that Everybody living on this Turkish Territory is a Turk.
Upon that, Atsız disclosed the secret studies and works of separatist Marxists in his serial articles "Konuşmalar, 1 (Talks, I)" (Edition 40), "Konuşmalar, II (Talks, II)" (Edition 41), "Konuşmalar, III (Talks, III)" (Edition 43), "Bağımsız Kürt Devleti Propagandası (Propaganda of Independent Kurdish State)" (Edition 43), "Doğu mitinglerinde perde arkası (Behind the Curtain in Eastern Demonstrations)" (Edition 47) and "Satılmışlar-Moskof uşakları (Sold People-Servants of Moscow)" (Edition 48) published as from 40th edition in Ötüken in April 1967. The public prosecution office launched an investigation against these articles. The first investigation by the public prosecutor did not place any blame on Atsız.
However, upon these articles, announcements prepared by separatist institutions in Ankara proclaiming separatism against Atsız were handed out in the streets and a Diyarbakır Senator of Adalet Party delivered an oppressive speech from senate rostrum.
As a consequence of these systematic efforts, in a period when Hasan Dinçer was the Minister of Justice, the ministry launched an inquiry and Atsız was sued. During the 6 years in which the action continued, 12 March memorandum was given and then martial law was proclaimed. While the separatists, communists and anarchists opposing the unity and inseparability of the Turkish nation and Land were put on trial with Martial Law Courts, Atsız, who drew attention to those people only 4-5 years before, was also put on trial.
After many sessions, the court sentenced Atsız, the owner of Ötüken, and its director Mustafa Kayabek to 15 months in prison. This decision which court chairman did not agree and which was reached as a result of 2 to 1 majority was appealed and quashed by the Court of Appeals. However, the court persisted in that decision reached with a majority of 2 to 1, the Court of Appeals approved the decision. Atsız and Mustafa Kayabek applied for correction of decision, however their wish was not accepted by the court. Thus, the decision was finalized.
Atsız, who wrote to Haydarpaşa Numune Hospital because he suffered chronic infarction, high blood pressure and severe rheumatism, was given a report by Haydarpaşa Numune Hospital a report that he cannot be put into prison. However, this report of 4-month was not accepted by Forensic Medicine and was modified as he can be put in prison in a penitentiary where there is an infirmary.