An investigation into an alleged plot by secularist ultranationalists to overthrow the Turkish government deepened with last week's arrest of senior military officers and the discovery of several weapons caches.

At the same time, there is growing concern that the probe – aimed at tackling longstanding, antidemocratic forces in Turkish politics – could lead to increased tension between the government and Turkey's powerful military.

"If the prosecution continues as we have seen it, we can have an extremely dangerous situation," says Gareth Jenkins, an Istanbul-based expert on Turkish security issues.

"You now have extreme distrust between the government and the military. What we don't want is a situation where the military believes the government is out to get it."

The investigation into the coup plot, which started in June 2007 and is known as "Ergenekon," has already resulted in the arrest of some 100 people, among them retired four-star generals and prominent politicians, journalists and academics. According to an indictment, the plotters were hoping to bring down the Islamist-rooted Justice and Development Party (AKP) by sowing enough chaos, through terror attacks and high-level assassinations, that the military would be forced to intervene.

Weapons caches found

In recent days, following sketches found in the homes of some of the suspects, police have uncovered two weapons caches buried on the outskirts of Ankara. Among the weapons were hand grenades, plastic explosives, and ammunition.

For many Turks, the investigation and the arrests – particularly of high-level military personnel – offer a chance to expose and unravel some of the work of the "Deep State," a phrase used to describe a shadowy zone where state interests intersect with lawless and corrupt elements of the bureaucracy, military, and the security establishment.

"I think this is a historical case. This is a good chance for the Turkish political system to put a stop to military interventions and to clean its ranks of these illegal affiliations between state authorities and gangsters and mafia types," says Sahin Alpay, a professor of political science at Istanbul's Bahcesehir University.

But the case, started in June 2007 after grenades were found in the Istanbul home of a retired military officer, is also creating new tensions between the AKP and the military, which sees itself as the ultimate guardian of Turkey's secular tradition and which has forced out of power four governments in the past.

The arrest last week of three retired generals and nine active officers led to the armed forces chief Gen. Ilker Basbug to call Prime Minister Recep Tayyip Erdogan for a surprise meeting.

Other parts of Turkey's secularist establishment, including the judiciary, are also crying foul over the course that the Ergenekon investigation is taking, saying the government is using it to silence its opposition and settle scores.

"We are witnessing a confrontation against the Republic's core values. This is a regime change, like in the Khomeini and Hitler eras," Deniz Baykal, leader of the main opposition Republican People's Party (CHP) said at a press conference after last week's arrests.

The Judges and Prosecutors Association (YARSAV) and the Istanbul bar association have also strongly criticized the way the investigation has been unfolding.

"We are concerned about the rule of law [in Turkey], as these people were detained because of their works and sensitivity over the democratic order, constitutional regime, secularism, and integrity of the state, in a way that could be assessed as revenge," Muammer Aydin, head of the Istanbul Bar, said recently.

But criticism of the case has not been limited to hard-line secularists.

Investigation tainted by politics?

The large number of arrests, which include some of the AKP's most vocal critics, and the dubious nature of the some of the evidence in the investigation have some observers asking if the Ergenekon case has become tainted by politics.

"I do not perceive Ergenekon as an empty investigation and I don't want to see it that way. In no way am I underestimating it. But if not put on the right track soon, I think it might turn into a big fiasco," Mehmet Ali Birand, a leading Turkish commentator, wrote recently.

Adds Jenkins, the military analyst: "[The Ergenekon investigation] started as a kernel of truth, but the AKP has seized on this as an opportunity to undermine the military and its secularist opponents and try to destroy their public reputation. With every step, it has become more politicized and anti-democratic."

Government officials have rejected claims that the probe has gone off track, saying its critics are simply not accustomed to seeing the rule of law extending to what had previously been untouchable figures.

Still, observers say that the enormity and importance of the case requires the government to move carefully.

"There really needs to be a scrupulous investigation. Everything has to be done by the book and in the right way," says Emma Sinclair-Webb, a Turkey researcher at the New York-based Human Rights Watch.

"On the other hand, you can't just caricature this whole process as simply being about a power struggle," she says.

"It's just too important of a chance for Turkey to grapple with a very dark history and get rid of a criminal apparatus within the state."