From the report (pdf), entitled "Between Fact and Fantasy: Turkey's Ergenekon Investigation":
Whether among those formally indicted as part of the Ergenekon investigation or those detained in the police raids and subsequently released without charge, many appear to have been guilty of nothing more than opposition to the AKP. In fact, there is no proof that the Ergenekon organization as described in the indictments exists or has ever existed.
Indeed, the indictments are so full of contradictions, rumors, speculation, misinformation, illogicalities, absurdities and untruths that they are not even internally consistent or coherent.
This is not to say that the Ergenekon investigation is simply a politically motivated fabrication. There is no reason to doubt that most of those involved in prosecuting the case sincerely believe in the organization’s existence and are unable or unwilling to see the contradictions and irrationalities that are endemic in the indictments. The indictments themselves appear to be the products of “projective” rather than deductive reasoning, working backwards from the premise that the organization exists to weave unrelated individuals, statements and acts into a single massive conspiracy. The more elusive the concrete evidence for Ergenekon’s existence is, the more desperate the attempts to discover it become. Rather than convincing the investigators that what they are looking for does not exist, this elusiveness appears merely to make the organization more fearsome and powerful in their minds; and further fuel their desperation to uncover and eradicate it.
A predilection for conspiracy theories is nothing new in Turkey and can be found across the political spectrum. Both a large proportion of AKP supporters and many of those in law enforcement genuinely believe that a malicious conspiratorial cabal – which most associate with the Deep State – has been not only manipulating the political process but supporting or guiding a large proportion of the political violence in the country. Amongst
AKP supporters, attention tends to focus particularly on violence carried out in the name of Islam; where their sincere horror at the carnage that is sometimes perpetrated in the name of their religion has created a culture of denial, and a refusal to believe that their fellow Muslims could be responsible.
The report takes a good look at some of the problems with the evidence, indictments and judicial procedures in the case. About the case's first indictment (there have been three released so far, and a fourth is expected), Jenkins writes:
The indictment was also marred not only by repeated examples of flawed reasoning but numerous absurdities and contradictions. Most remarkably, despite its extraordinary length, the indictment produced no evidence that the Ergenekon organization it described even existed, much less that the accused were all members and engaged in a coordinated terrorist campaign to overthrow the government.Indeed, rather than being based on deductive reasoning, the indictment appeared to project onto a collection of disparate events and individuals – not all of whom are necessarily innocent of any wrongdoing – a conspiracy theorist’s template of a ubiquitous, and almost omnipotent, centrally controlled organization which had not only penetrated every sphere of public life but been responsible for virtually every act of politically-motivated violence and terrorism in modern Turkish history….
…. some of the claims in the indictment about Ergenekon’s deeds and ambitions extended beyond the bounds of credibility. For example, the indictment claimed that the organization had met with the then U.S. Vice President Dick Cheney to discuss toppling the AKP government and replacing it with a more acceptable alternative. Even more absurdly, the indictment maintained that investigators had uncovered evidence that the “Ergenekon Terrorist Organization” planned to “manufacture chemical and biological weapons and then, with the high revenue it earned from selling them, to finance and control every terrorist organization not just in Turkey but in the entire world.”
In the end, Jenkins calls the Ergenekon case a "wasted" opportunity:
From a broader perspective, the public debate triggered by the discovery of the crate of grenades in Ümraniye in June 2007 could have provided an opportunity for the establishment of an independent truth commission which could perhaps have enabled Turks – including both secular nationalists and Islamists – to come to terms with the realities of recent Turkish history. But, in the short-term, a more pressing concern is not the wasted opportunity for Turkey to confront its past but what the Ergenekon investigation might be saying about its future, and the disturbing questions it raises about the prospects for democracy and the rule of law in the country.
Clearly, there are other views out there about the merits and the strength of the evidence of the Ergenekon case, but Jenkins's report is highly recommended reading for anyone interested in this complex story.