He was under indictment in the OdaTV case of the Ergenekon trials; his cause has been taken up by English PEN, an association of writers fighting for freedom of expression.

[1] In 1998, he was hospitalized "after a pro-police mob, furious about a murder conviction against several cops in a torture case, attacked the victim’s lawyers, the prosecutor, and journalists.

[1] Şık accused Hayko Bağdat [tr], an Armenian-Turkish activist who is the only one taking stage with a steelvest in the history of Germany including the Nazi regime,[13][14] of being an agent of the Gulen movement.

[15] Bagdat later on claimed that Şık's accusation put his life in danger and caused threats from the Turkish deep state, especially from the Ergenekon sympathizers.

[19] He co-authored an extensive report for the party investigating the ties, alleged by Sedat Peker, between the interior minister Süleyman Soylu, the organized crime and the deep state in Turkey, which was published as a book under the title The Wall (Duvar in Turkish).

Bakırköy 2nd Court of First Instance in İstanbul ruled that the article titled “The military should withdraw its hand from internal security” in the 8 February 2007 edition of weekly Nokta should be evaluated as “harsh criticism” and its publication does not constitute a criminal offence.

[5] He was indicted twice with charges of insulting Prime Minister Binali Yıldırım due to his public duties; in one of these cases, he was ordered to pay 4,000 Turkish liras; in another, the prosecutor demanded his imprisonment for up to two years and four months.