The morning rush had begun at the health ministry’s morgue in Baghdad, and by 9.30am last Thursday 36 coffins already lined the street outside. A muffled wailing came from the minibuses parked nearby where women shrouded in black waited to go inside and search for loved ones, knowing too well what they would find.

The single-storey Al-Tub al-Adli morgue, whose nondescript appearance belies the horrors within, has become synonymous with the seemingly unstoppable violence that has turned Baghdad into the most frightening city on earth.

It is here that bodies from the nightly slaughter are dumped each morning. The stench of decaying flesh, mingled with disinfectant, hits you at the checkpoint 100 yards away.

Each corpse tells a different story about the terrors of Iraq. Some bodies are pocked with holes inflicted by torturers with power drills. Some show signs of strangulation; others, with hands tied behind the back, bear bullet wounds. Many are charred and dismembered.

So far this year, according to health ministry figures, the mortuary has processed the bodies of about 6,000 people, most of whom died violently. Some were killed in American military action but many more were the victims of the sectarian violence that US and Iraqi forces are struggling to contain.

For all the coalition’s recent successes in securing elections that brought a new government to power and in killing Abu Musab al-Zarqawi, the commander of Al-Qaeda in Iraq, the morgue remains a chilling reminder of the scale of the challenge ahead.

It receives 20 to 30 bodies on a quiet day. Last month it processed a record 1,384. Most autopsies have been cancelled; there are simply not enough doctors or officials to cope.

For Iraqis who suffer the loss of a family member, a dreaded ritual ensues. Everyone knows there is no point in reporting a missing person to the police — no action will be taken. The first stop is always the morgue. The lucky ones find a body straight away. For others, the morning walk past the coffins has to be repeated. Their search can last for days.

As a former trauma specialist in a hospital casualty department, Dr Baker Siddique, 29, thought he was inured to scenes of carnage. But nothing he had witnessed prepared him for a visit to a pathologist friend working at the mortuary.

“I saw a street packed with people and coffins standing up vertically,” he said. “There wasn’t enough room to lie them horizontally.”

His voice faltered and his eyes filled with tears as he recounted the agony of a woman in black who discovered the bodies of her four sons that day.

“I have never heard screams of pain like that,” he said. The woman collapsed on the floor, throwing dirt over her head — a gesture of grief and helplessness that has become tragically commonplace in Iraq.

As the doctor talked to his friend, a police pickup truck pulled up with a dozen or more bodies piled in the back. “I could not believe that the dead were brought in such a way,” Siddique said. “They were one on top of the other like animal carcasses.”

When the police found that no porters were available to help, they threw the bodies off the truck. It was then that Siddique noticed the corpses of two boys aged about 12 lying in the pile on the ground.

“Each had a piece of knotted green cloth tied around his neck and I could see they’d been strangled,” the doctor said. He also noticed round holes that were slightly inflamed in several parts of their body, a sign that they had been tortured with electric drills before being killed. “Even their eyes had been drilled and only hollow sockets remained,” he said.

When he pointed out the injuries to his friend, the pathologist shrugged and took another drag on his cigarette, saying this was now routine.

“We have turned into a zoo,” Siddique told me. “What level have we sunk to, to kill people in such a manner and hardly to notice any more?”

The doctor sat with me for a long time, silent and seemingly unable to move. Then he began to give voice to his thoughts.

“Did those children scream in pain? Did the torturers laugh as they drilled? If we ever had a just cause as a country occupied by foreigners, it was lost the moment the resistance started beheading and drilling human beings. No matter how noble their cause when it began, they have now reached a dead end.”

After a relentless series of increasingly difficult and dangerous visits to Iraq, I had hoped to stay away from Baghdad for a few months. Yet Zarqawi’s death appeared to represent a breakthrough for the coalition. With a new prime minister, Nouri al-Maliki, in power, I was not the only one to feel the time might be ripe to return. President George W Bush also arrived in the city last week — three years after he had declared “mission accomplished” for the coalition effort in Iraq.

Although US officials were generally cautious in their assessments of a wounded insurgency, there was no mistaking the revived morale of the forces. Backed by tanks and armoured vehicles, more than 75,000 soldiers and Iraqi policemen launched a fresh attempt to retake the streets of Baghdad from the militias and jihadists who have brought the city to its knees.

Yet it quickly became clear as I sought out both victims and perpetrators of the violence that the surge in military morale is not shared by many civilians.

Samir Mehdi Matar, a 40-year-old father of four, is a Shi’ite schoolteacher. Married to a Sunni woman he fell in love with at university, he has never been tempted to side with any of the warring Muslim factions.

He lived in a mostly Christian district where few of his neighbours were concerned about his religious or political affiliations. He kept pictures of Shi’ite imams in his home, but claims never to have flaunted his religion.

Shortly after leaving for work last April he received a phone call. His house had been wrecked by an explosion. His two daughters, Samaa, 16, and Zahraa, 4, were killed by a bomb that had been placed on a windowsill below the room where they slept.

“I went to the hospital refrigerator and pulled their bodies out,” Samir said. “I kissed each one of them on the head. It was my final farewell.”

The death certificate for each of the girls records the cause as “terrorist explosion”.

Samir wanted me to see the younger child and handed me his mobile phone. A video clip showed a little girl with big brown eyes chuckling as she naughtily pretended to smoke a cigarette. “She was an incredible child,” he said.

After her death a group of Shi’ite militiamen visited Samir and asked him to provide names of any Sunnis who might have carried out the attack. “Give us 40 names if you want and we will see to it that they are eliminated,” he was told.

Samir thanked them but told them he had no suspects. “Those who come seeking to spill further blood in an already broken nation are failures,” he said. “What would the spilling of further blood achieve?”

Yet he acknowledges that the cycle of vengeance will not be easy to break. “Our country has collapsed and what collapses is hard to revive,” he said.

Najda Abdul Razzak makes no apology for wishing to tear out the eyes of the killer of her son Hani, a 31-year-old Sunni professor of engineering at Baghdad University.

Najda was in her kitchen preparing breakfast last week when her son answered a ring at the door and died in a hail of gunfire. He was hit six times in the forehead, mouth, neck, chest, right arm and leg. “I don’t understand why,” said Najda. “Is it because he was a pious Muslim?”

She sobbed as she mourned her loss. “Not even your house is a sanctuary any more,” she said.

She presumes that her son’s killers were Shi’ites. “If I find his killer I will bite him and shred him to pieces with my teeth,” she cried in anguish.

There are countless stories like this in Baghdad. The main topic of conversation in most households is death — who is the latest to have been killed, what depraved technique was used and whether it is safe to go out.

The day before coalition forces launched their latest security crackdown, dubbed Operation Forward Together, I went to see some Sunni insurgents. The main topic of conversation was the killing of Zarqawi but it barely seemed to have dented their enthusiasm for revolt.

On the contrary, one man assured me that Zarqawi’s death might finally prove to the Americans and the world that the Iraqi insurgency was more than an Al-Qaeda-led plot and would not cease with any one man’s death.

If the story of Abu Muawiya is any guide, the killing is not about to stop. Abu Muawiya claims to be a “specialist” in killing Shi’ites and boasts about “cleansing” his mainly Sunni Amiriya neighbourhood of its Shi’ite residents.

“Every day we have to kill a Shi’ite to show them who we are and that we mean business,” he told a Baghdad contact who cannot be named. “Nobody can stop us.”

When the contact saw a body that had apparently been left to rot on the street, he asked Abu Muawiya why nobody had moved it. He was told that it was because the body was Shi’ite and anyone who touched it would be killed.

A few hours later the contact saw a man shot dead for removing a piece of cardboard hiding the face of a second body and informing the victim’s family.

Abu Muawiya showed no remorse. “We do not want their bodies cleared from the streets,” he said. “We leave them there for the dogs to eat, just as they dump Sunni bodies in rubbish heaps to be devoured by animals.”

Rival militias — frequently backed by sympathisers in the Iraqi army and police — have begun to compete with each other in “cleansing” districts and inflicting atrocities.

“We’re always having to invent new methods of torturing people to death,” said a 32-year-old airport worker who also claims to command the interrogation section of a militia cell loyal to Sheikh Moqtada al-Sadr, the rebel Shi’ite cleric.

My friends had warned me of the worsening sectarian hatred in Iraq, but I was chilled to discover how widespread such malevolence had become. Shi’ites blame the Sunnis for the deteriorating security while Sunnis accuse the Shi’ites of colluding with Iran.

There was a time when, as visitors to Iraq, we mainly worried about falling into the hands of Zarqawi’s supporters. Now we fear everyone, everywhere. Hundreds of thousands of Iraqi middle-class professionals are fleeing to Jordan, Lebanon and the Gulf for fear of being targeted by death squads.

These are scarcely promising conditions for the revitalised coalition effort, but both Washington and the new administration in Baghdad appear determined to grasp the opportunity that the death of Zarqawi has presented.

In one sense they are off to a good start. The intelligence operation that tracked down Zarqawi has netted a treasure trove of leads on insurgent cells and hideouts. The coalition has also benefited from a sharp increase in intelligence tips from Iraqi civilians, up to 4,400 a month, compared with 1,700 a month a year ago.

Last week’s crackdown included a ban on weapons and a curfew extended by 4½ hours from 8.30pm until dawn. There were early signs that the increased checkpoints and random searches of vehicles were reducing the level of violence.

US officials are hoping to maintain a stranglehold on so-called “red” areas before launching “clear and hold” operations to drive insurgents out of the city. They are aware that similar operations in the past have merely shifted insurgents elsewhere, but Washington believes that a prolonged summer offensive based on solid intelligence will at last begin to isolate the foreign terrorist element of the insurgency.

“The fact is we are disrupting their infrastructure, the bomb-making factories and the guys who are turning out IEDs (improvised explosive devices),” said Dan Goure, a military analyst at the Lexington Institute in Washington. “It is becoming harder for them to move around and there aren’t a lot of good hiding places left.”

Goure foresees a four to five-month offensive that stands at least a chance of changing the momentum of the war. “If you can crack the insurgent structure and organisation, you can dissuade others from joining and slowly put together a string of successes, large or small,” he said.

Yet he and other analysts agree that long-term success depends on the commitment of Iraqi forces whose allegiances remain highly suspect. “Senior Iraqi officials make it clear that they see the threat as both insurgent and a mix of militias and local security forces,” said Anthony Cordesman, a regional specialist at the Washington-based Center for Strategic and International Studies.

Cordesman added that for any operation to have real meaning “it has to go far beyond manning checkpoints, establishing a visible presence and creating the image of security”.

He likened the counter- insurgency operations to police drug raids. “They are meaningless if they simply sweep in, make dramatic seizures and then leave and allow the problem to resurface,” he said. The latest operation could prevail only “if Iraqi police and the Iraqi government establish a lasting presence and control in red areas”.

In Baghdad, the Iraqi head of operations at the defence ministry said Iraqi commanders were aware that some of their units might already have been infiltrated by sectarian militants.

Major General Abdul Aziz Mohammed Jassem said special intelligence units were being deployed to every base and checkpoint to monitor Iraqi troop activity, and vows of allegiance to the country and constitution would be demanded within 48 hours.

Sunni politicians are also concerned that the new security offensive will provide a cover for persecution by the Shi’ite-dominated army and other militias.

“We shall watch the execution of the plan very carefully,” said Thafer al-Anni, a Sunni MP. “It can only work if accompanied by other measures, including the cleansing of the security apparatus.”

Whatever happens in the coming weeks as US forces fight to turn the tide, it has all come too late for Mohammed Saleh al-Duleimi, a 61-year-old Sunni businessman who concluded a few weeks ago that it was too dangerous for him and his family to stay in Baghdad.

The day before he was due to leave for Turkey, he went to find an electrician who could help to shut down his house. He was found two days later in the morgue with a bullet hole in the back of his head and his hands tied behind his back.

Some names have been changed to protect the people concerned Additional reporting: Tony Allen-Mills, New York

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