It was 7.30 am on a Monday when Ayşe Yıldırım’s phone started ringing. The columnist at Cumhuriyet, Turkey’s last leading newspaper critical of the government, picked up the phone.

It was her boss, the newspaper’s editor-in-chief, Murat Sabuncu, one of a dozen of her colleagues who would be in a jail cell by the end of the day. “He said to me: ‘The police are in my flat and they’re going to arrest me,’” she said.

Five months after a coup attempt aimed at toppling the administration of the Turkish president, Recep Tayyip Erdoğan, Turkey still appears shaken by the turmoil. Tens of thousands of bureaucrats, military officers, police officials, judges and academics have been purged over alleged links to Fethullah Gülen, a US-based preacher whose movement is believed by the government and many in the opposition to have been behind the attempted putsch.

Many media outlets and non-governmental organisations have been shut down, accused of fomenting terrorist propaganda on behalf of Gülen’s organisation or the Kurdistan Workers’ party (PKK), a separatist group fighting an insurgency against the Turkish state.

Critics say the purges have gone far beyond the scope of Gülen and his movement, encompassing peaceful dissidents who oppose the president, who is seeking to revise the Turkish constitution to transform the country from a parliamentary democracy into a presidential system.

Cumhuriyet is a case in point. Founded in 1924, it has long been a symbol of Turkey’s secular order, but in recent years it has found itself in the government’s crosshairs. Its former editor-in-chief Can Dündar was arrested last year as punishment for a report claiming that the national intelligence service, MIT, was sending trucks filled with armaments to rebel fighters in Syria under the guise of humanitarian aid, and for the newspaper’s reporting on a 2013 corruption scandal targeting Erdoğan’s inner circle.

This month 13 journalists, lawyers and board members, including Cumhuriyet’s chief executive, were detained as part of a terrorism investigation in which prosecutors claim the newspaper’s top staff were “committing crimes in the name of” Gülen and the PKK, without going so far as to accuse them of being members of either group.

Aydin Engin is escorted by plainclothes police officers from his home on 31 October. Photograph: AFP/Getty Images

For staff at Cumhuriyet, the aim of the campaign is quite clear. “They want to silence Cumhuriyet because it is now the only newspaper that isn’t a party organ,” said Aydın Engin, a columnist and former editor-in-chief. “They’re trying to silence that last remaining castle, and the rule of law is in the deep freezer.”

Engin, who lived in exile in Germany for years and has been imprisoned half a dozen times for his political writings, was rounded up in the latest operation and then released because of his age. He chuckles when asked about his interrogation, which included accusations of committing crimes on behalf of the PKK and the Gülenists, and even questions about working for the CIA. “Which is insane,” he said. “But I don’t think the prosecutors knew the meaning of the word oxymoron.”

The mood outside his office is more sombre. The newsroom feels subdued after the latest arrests, and reporters can be seen chainsmoking nervously en masse in the newspaper’s courtyard. A police cordon blocks the road towards Cumhuriyet’s offices in Istanbul, and a banner hung next to a large portrait of Mustafa Kemal Atatürk, the founder of the republic, on the building’s facade reads: “There is courage here.”

Journalists in Turkey have long complained of a crackdown on the press and widespread intimidation, particularly against Kurdish media outlets. Newspapers and TV stations accused of harbouring sympathies to the Gülenists have been shut down and taken over by government-appointed trustee boards, which often transform them into loyalist outlets.

After the arrests, the government can now legally appoint a trustee board to run Cumhuriyet, but it appears to be hoping the intimidation will spur a change in editorial policy.

The deputy prime minister, Veysi Kaynak, said the government was deliberately avoiding a takeover. “We want the Cumhuriyet newspaper to fix its own mistake,” he told parliament.

That “mistake” appears to be an editorial policy that is opposed to the government on two key issues: its stance on the purges after the coup, which it has described as a witch-hunt, and its stance on the Kurdish issue, where it has endorsed a peaceful solution to the conflict despite the abandonment of peace talks and growing violence in Kurdish areas.

A demonstration in support of Cumhuriyet in front of its headquarters in Istanbul. Photograph: Yasin Akgul/AFP/Getty Images

Twenty years ago, readers would have been surprised to see Cumhuriyet endorsing peace with the Kurds. In the early 1990s its powerful chairman, Ilhan Selçuk, was close to Turkey’s top generals and ultra-nationalists and wholly backed a security response to Kurdish demands.

After his death in 2010 the paper urged democratic reforms in Turkey, but even as they write columns opposing Erdoğan’s policy, its writers are staunchly against the coup and believe Gülen was behind it.

According to the minutes of the journalists’ interrogations, prosecutors repeatedly questioned them about editorial policy changes and whether they were sending hidden messages in their headlines endorsing the coup. “It’s tragicomic,” said Yıldırım.

The situation they find themselves in appears to be surreal to Yıldırım and her colleagues. On the day of the arrests, as they gathered in the newsroom, more and more staff members were called to the police station to testify or be detained.

One of those in the newsroom that day was Bülent Özdoğan, the managing editor, who has been at Cumhuriyet for 16 years. There are dark circles under his eyes and his voice is hoarse from exhaustion.

“We became the news. I don’t know if it’s good or not,” he said. “We want to report, not be the news itself. We will go on to do a good newspaper, that’s all I can say.”