Never before has such a senior uniformed figure faced trial for crimes committed during Turkey’s bloody counter-insurgency campaign against ethnic Kurdish separatists. Lurid testimony has been given of severed ears threaded as prayer beads and corpses disposed of in wells of acid. The web of evidence includes jailhouse testimony from a brother of Cizre’s former mayor and the discovery of human remains.

For over 25 years the Kurdistan Workers’ Party or PKK, a group designated a terrorist organization by Turkey, the European Union and the United States, has fought an armed struggle in pursuit of a separate Kurdish state.

The conflict has cost tens of thousands of lives and led to a stream of internal migration away from the affected areas.

While human rights campaigners and the families of the dead have welcomed the Temizoz trial, the case also highlights the problems Turkey faces in reaching any settlement with its past. Prime Minister Tayyip Erdogan, the leader of the Islamic-leaning Justice and Development Party or AK, has tried to expand the rights of minority Kurds.

Nationalist rivals fiercely oppose Erdogan’s initiatives, but so do many AK supporters. An election is due next year, and the AK has to protect its vote bank to win a third term.

The influence of conservative, secular nationalists opposed to AK has waned, but they remain a force to be reckoned with in a country that has become increasingly polarized since the AK shot to power in 2002.

The old elite’s strongholds remain the military and the judiciary and the courts have become a battleground.

“Turkey is dealing with issues of transitional justice while the transition is not over yet,” said Gerald Knaus, a fellow at the Carr Center for Human Rights Policy at Harvard University.

While South Africa and some Latin American nations have tried to address past human rights abuses after a complete change of regime, Turkey is trying to address its past without such a dividing line between old and new governments.

At the same time it is taking steps to strengthen its democracy, having seen its military topple four governments in the last 50 years.

“What is happening in Turkey at the moment does not happen usually in countries where there is no big rupture,” said Kerem Oktem, an academic at St. Anthony’s College in Oxford.

For decades the idea endured that the military stood above civilian authorities as guardian of the secular values of the modern republic founded in 1923 by Mustafa Kemal Ataturk.

Today that notion is changing. There is still enormous respect for the military and Ataturk’s portrait adorns classroom and office walls across the country.

But Turks, confident that democracy will bring prosperity and opportunity, do not want any more coups, and many believe the armed forces must be subject to the same laws as the rest of the country. The ruling AK party has drafted constitutional amendments that would, among other changes, make military officers liable for prosecution in civilian, rather than military, courts.

Much of the current focus on the past stems from the Ergenekon investigation, a probe into the supposed ‘deep state’ — a secret group of hard-line nationalists in the security forces and bureaucracy determined to uphold secular values.

The investigation began in 2007 and as it gained ground, Turks watched in amazement as a procession of senior military figures, both serving and retired, appeared before prosecutors.