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This is MORNING EDITION from NPR News. I'm Ari Shapiro.

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Turkey is witnessing what may be the most important trial in the country's history. The subject is the nature of Turkey itself. That's because the trial is over an alleged conspiracy to overthrow a democratically elected government. That conspiracy allegedly included members of the military, and if it's true, such a conspiracy would be nothing the military hasn't done before.

NPR's Deborah Amos reports from Istanbul.

(Soundbite of whistle blowing)

DEBORAH AMOS: Thousands march through Istanbul each week to demonstrate support for what Turks call the trial of the century.

(Soundbite of chanting)

Eighty-six defendants, so far, charged with belonging to a secret terrorist organization. Those arrested include retired generals, journalists and politicians. The indictment alleges a conspiracy to bring down the ruling justice and development party, the AKP. In 2002, the AKP won elections for the first time in a landmark vote. The AKP is rooted in conservative Islam. The elections unsettled the country's secular elite, including the military.

The coup plot had a name, according to the indictment, with roots in Turkish mythology that's come to mean a secret organization within the state.

Mr. MEHMET ALI BIRAND: Ergenekon. It's a bit difficult to swallow, but doesn't matter. It's like Ergenekon.

AMOS: That's Mehmet Ali Birand, a television personality and a newspaper columnist. He describes the alleged plot to murder members of Turkey's political and cultural elite, setting the stage for a military take over.

Mr. BIRAND: I'm happy that Ergenekon is out of the closet. We knew it but we couldn't touch it. For the first time we are discussing that the military's involvement in the politics. We are discussing that very much.

AMOS: There is history in this uniquely Turkish story. The country has had three successful coups by a military that sees itself as the protector of Turkey's secular state, a role that now seems in question, says Henri Barkey, a Turkey expert at Pennsylvania's Lehigh University.

Professor HENRI BARKEY (Lehigh University, Pennsylvania): It has diminished and tarnished the military, because so many of its former generals are caught up in this thing. So in that sense it is quite damning.

AMOS: I'm standing outside the courtroom where the Ergenekon trials take place. The lawyers, and there are many lawyers, arrive by bus from Istanbul. There are no cell phones or recording devices allowed inside the courtroom. There are two security checks and they are very heavy. I'm going inside to hear a case.

In the wood paneled courtroom, the judges hear the testimony of the latest defendant - on this day, a computer programmer charged in the plot. There are more than a dozen reporters in the courtroom.

Mr. COKSAL GOCHE(ph) (Television correspondent): My name is Coksal Goche. I'm correspondent for Turkish television.

AMOS: Goche reports on an indictment so complex and confusing, some defendants complain they don't know what they're charged with. But a recent opinion poll showed a majority of Turks, 61 percent, believe the coup attempt was real, says Goche.

Mr. GOCHE: Most of the Turkish people think that they are opposite of democracy.

AMOS: The people who were in Ergenekon?

Mr. GOCHE: Yes. We must solve this problem.

(Soundbite of beep)

AMOS: In any conspiracy investigation there seems to be a newspaper that digs deeper than the rest. Watergate had the Washington Post. In Turkey it's Taraf, a politically liberal newspaper with offices at the top floor of a bookstore and an armed guard at the door.

Yasemin Congar is the lead reporter on Taraf's investigative team.

Ms. YASEMIN CONGAR (Reporter, Taraf): We are a small newspaper. It's a newspaper that created a lot of noise for its size. Some of us have received death threats.

AMOS: Have you personally gotten death threats?

Ms. CONGAR: In the past, yes.

AMOS: But in the past, says Congar, investigations into sensitive subjects were blocked. For example, the murder of a Turkish-Armenian journalist and the harsher aspects of the military campaign against Kurdish separatists in the southeast. This is also part of Ergenekon says Congar.

Ms. CONGAR: There is a lot of dirt, there are many corpses, there are dead people, and now we're digging it out, and we are finding ammunition everywhere, like hand grenades and C-4 exploding devices, you name it.

AMOS: The discovery of several arms dumps and the mounting evidence has embarrassed the generals. High-ranking arrests have caused tension between the government and the military. And lately, some Turkish commentators complain that the trials have gone too far - an attempt by the moderate Islamist ruling the country to discredit the secular army and silence the secular political oppositions, says Mehmet Ali Birand.

Mr. MEHMET ALI BIRAND (Turkish television commentator): They are trying to push the opposition to this government into a corner, saying that - hey, be careful, you can be detained. So that's bad. It's getting too far.

AMOS: So far one Turkish court agreed. A retired four-star general was released last week after seven months in jail. The court ruled there was not enough evidence to keep him locked up.

Deborah Amos, NPR News, Istanbul.

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