If I had to guess, I'd say that there were 200 of us milling outside the courtroom where Orhan Pamuk was to have been tried this past Friday morning. The Turkish intelligentsia was there in force - at least, that part of the intelligentsia that campaigns for human rights. There were more than a dozen European parliamentarians, and journalists from all over the world. So at first we just ignored the woman spouting fascist venom at the top of the stairs. But when the defendant arrived and she rapped him on the head with a rolled-up plastic folder, we could not help but wonder. Who'd let her in?

By now the 20-odd riot police were herding us towards the courtroom. When the room filled to the brim and the door slammed shut, the crowd kept moving forward. I almost got crushed. Meanwhile, at the other end of the corridor, a group of nationalist fascist agitators had formed a ring around a target "traitor" while the riot police watched blankly. After a nod from a man, said by some to be a plainclothes policeman, they quietened down, only to move on to another target, and then another.

Why were they allowed to stay among us? What to make of the nationalist lawyers whose foaming representations against Orhan Pamuk took up most of the 50-minute hearing? After asking the judge to clear the room of meddling Europeans, one of them socked Denis McShane in the eye. McShane and several other EU parliamentarians were assaulted again later as they left the building. Then came the eggs and the pelting of stones, which the Turkish press politely described as having been thrown "from a distance".

Though the right-wing tabloids rejoiced that the "fearful", "white-faced" author and his meddling European friends got their comeuppance, the more responsible newspapers expressed shame and dismay at the mayhem, rightly saying that it had damaged Turkey's image abroad, perhaps irreparably. A handful of columnists dared to ask why security had failed so dismally, but no one was venturing theories. There was no need: they'd got the message.

I did, too, so let me pass it on. This was not a security failure, nor was it a case of a government or a judicial system "shooting itself in the foot": this was a carefully orchestrated attempt to insult and intimidate Pamuk's supporters, and most especially the EU parliamentarians who had come to observe his trial. It is no accident that it happened in full view of the world media, just as it is no accident that Turkey comes out of it looking like an old-style authoritarian regime. For that is exactly what it is, and that is how a certain very powerful élite would like it to remain.

The army has been the dominant force in the Turkish Republic for as long as there has been a republic. It sees itself as the guardian of Mustafa Kemal Ataturk's founding vision; if it feels a government is straying from the Kemalist path, it feels duty bound to step in. In 1960, it did not just remove the then prime minister from office; it had him and two of his ministers hanged. Then it drafted a new constitution that greatly increased the military's role in politics. Since then it has stepped in twice - in 1971 and in 1980. Turkey's current constitution is the one the generals drafted in the early Eighties before stepping back out again. Both the penal code that expired earlier this year and the supposedly EU-friendly code that has replaced it put serious curbs on freedom of expression.

One of the main conditions of EU entry is that Turkey must cease to be a "tutelary" or "guided" democracy. This means rolling back the army's role in politics. If Turkey joins Europe, the military stands to be the biggest loser. For certain patriotic and well-placed militarists, EU entry is not just a threat to their power base but an out-and-out betrayal of Kemalism as they understand it.

We are not to know if these faceless, nameless parties are in touch with the prosecutors who have now charged more than 50 writers, editors, and academics for publicly insulting the judiciary, the army, or Turkishness itself. But there are many new and dark rumours about the "deep state", the network of security forces, intelligence operatives and fascist paramilitaries that many view to be the driving force of Turkish politics. After a recent bungled bombing of a Kurdish bookstore in a city in the south-east, there are even a few shreds of proof.

Europe is not the Turkish army's sole preoccupation. There is the deepening crisis in Cyprus, the prospect of an autonomous Kurdish state in northern Iraq, and the strain in its relations with its longtime bankroller, the US. Hemmed in on all sides by troublesome and meddling foreigners, it may be losing its patience.

The writer is Orhan Pamuk's English translator