Two years ago Jalal Yako, a Syriac Catholic priest, returned to his home town of Qaraqosh to persuade members of his community to stay in Iraq and not to emigrate because of the violence directed against them.

"I was in Italy for 18 years, and when I came back here my mission was to get Christians to stay here," he says. "The Pope in Lebanon two years ago had established a mission to get Christians in the East to stay here."

Father Yako laboured among the Syriac Catholics, one of the oldest Christian communities in the world, who had seen the number of Christians in Iraq decline from over one million at the time of the American invasion in 2003 to about 250,000 today. He sought to convince people in Qaraqosh, an overwhelmingly Syriac Catholic town, that they had a future in Iraq and should not emigrate to the US, Australia or anywhere else that would accept them. His task was not easy, because Iraqi Christians have been frequent victims of murder, kidnapping and robbery.

But in the past six months Father Yako has changed his mind, and he now believes that, after 2,000 years of history, Christians must leave Iraq. Speaking at the entrance of a half-built mall in the Kurdish capital Irbil where 1,650 people from Qaraqosh have taken refuge, he said that "everything has changed since the coming of Daesh (the Arabic acronym for Islamic State). We should flee. There is nothing for us here." When Islamic State (Isis) fighters captured Qaraqosh on 7 August, all the town's 50,000 or so Syriac Catholics had to run for their lives and lost all their possessions.

Many now huddle in dark little prefabricated rooms provided by the UN High Commission for Refugees amid the raw concrete of the mall, crammed together without heat or electricity. They sound as if what happened to them is a nightmare from which they might awaken at any moment and speak about how, only three-and-a-half months ago, they owned houses, farms and shops, had well-paying jobs, and drove their own cars and tractors. They hope against hope to go back, but they have heard reports that everything in Qaraqosh has been destroyed or stolen by Isis.

Christians who fled Mosul pray at a church in Qaraqosh (AFP/Getty)

Some have suffered worse losses. On the third floor of the shopping mall in Irbil down a dark corridor sits Aida Hanna Noeh, 43, and her blind husband Khader Azou Abada, who was too ill to be taken out of Qaraqosh by Aida, with their three children, in the final hours before it was captured by Isis fighters. The family stayed in their house for many days, and then Isis told them to assemble with others who had failed to escape to be taken by mini-buses to Irbil. As they entered the buses, the jihadis stripped them of any remaining money, jewellery or documents. Aida was holding her three-and-a-half month old baby daughter, Christina, when the little girl was seized by a burly IS fighter who took her away. When Aida ran after him he told the mother to get back on the bus or he would kill her. She has not seen her daughter since.

It is not the savage violence of Isis only that has led Father Yako to believe that Christians have no future in Iraq. He points also to the failure of both the Iraqi government and the Kurdistan Regional Government (KRG) to defend them against the jihadis. Christians in Iraq have traditionally been heavily concentrated in Baghdad, Mosul and the Nineveh Plain surrounding Mosul. But on 10 June some 1,300 Isis fighters defeated at least 20,000 Iraqi army soldiers and federal police and captured Mosul. The army generals fled in a helicopter. In mid-July Christians in the city were given a choice by Isis of either converting to Islam, paying a special tax, leaving or being executed. Almost all Christians fled the city.

Kurdish peshmerga moved into Qaraqosh and other towns and villages in the Nineveh Plain. They swore to defend their inhabitants, many of whom stayed because they were reassured by these pledges. Father Yako recalls that "before Qaraqosh was taken by Daesh there were many slogans by the KRG saying they would fight as hard for Qaraqosh as they would for Irbil. But when the town was attacked, there was nobody to support us." He says that Christian society in Iraq is still shocked by the way in which the Iraqi and Kurdish governments failed to defend them.

A Christian refugee prays in Irbil (AFP/Getty)

Johanna Towaya, formerly a large farmer and community leader in Qaraqosh, makes a similar point. He says that up to midnight on 6 August the peshmerga commanders were assuring the Syriac Catholic bishop in charge of the town that they would defend it, but hours later they fled. Previously, they had refused to let the Christians arm themselves on the grounds that it was unnecessary. Ibrahim Shaaba, another resident of the town, said that he saw the Isis force that entered Qaraqosh early in the morning of 7 August and it was modest in size, consisting of only 10 vehicles filled with fighters.

At first, IS behaved with some moderation towards the 150 Christian families who, for one reason or another, could not escape. But this restraint did not last; looting and destruction became pervasive. Mr Towaya says that the Isis authorities in Mosul started "giving documents to anybody getting married in Mosul to enable them to go to Qaraqosh to take furniture [from abandoned Christian homes]."

As so many had fled, there are few who can give an account of how IS behaved in their newly captured Christian town. But one woman, Fida Boutros Matti, got to know all too well what Isis was like when she and her husband had to pretend to convert to Islam in order to save their lives and those of their children, before finally escaping. Speaking to The Independent on Sunday in a house in Irbil, where they are now living, she explained how she and her husband Adel and their young daughter Nevin and two younger sons, Ninos and Iwan, twice tried to flee but were stopped by Isis fighters.

Timeline: The emergence of Isis Show all 40 1 /40 Timeline: The emergence of Isis Timeline: The emergence of Isis 2000 Abu Musab al-Zarqawi (pictured here) forms an al-Qaeda splinter group in Iraq, al-Qa’eda in Iraq. Its brutality from the beginning alienates Iraqis and many al-Qaeda leaders. Timeline: The emergence of Isis 2006 Al-Zarqawi is killed in a U.S. strike. Al-Zarqawi’s successor, Abu Ayyub al-Masri, announces the creation of the Islamic State in Iraq (ISI). Reuters Timeline: The emergence of Isis 2009 Still al-Qaeda-linked ISI claims responsibility for suicide bombings that killed 155 in Baghdad, as well as attacks in August and October killing 240, as President Obama announces troop withdrawal from Iraq in March. Getty Images Timeline: The emergence of Isis 2010 Abu Bakr al-Baghdadi becomes head of ISI, at lowest ebb of Islamist militancy in Iraq, which sees last U.S. combat brigade depart. Timeline: The emergence of Isis 2012 In Syria, protests (pictured here starting in Daree) have morphed into what president Assad labelled a “real war” with emergence of a coalition of forces opposed to Assad’s regime. Syria group Jabhat al-Nusra are among rebel groups who refuse to join, denouncing it as a “conspiracy”. Bombings targeting Shia areas, killing more than 500 people, spark fears of new sectarian conflict. Sunni Muslims stage protests across country against what they see as increasingly marginalisation by Shia-led government. AP Timeline: The emergence of Isis 2013 Al-Baghdadi renames ISI as the Islamic State in Iraq and Syria, or Isis, as the group absorbs Syrian al-Nusra, gaining a foothold in Syria. In response, al-Qaeda chief Ayman al-Zawahiri (Bin Laden’s successor) concerned about Isis’ expansion orders that Isis be dissolved and ISI operations should be confined to Iraq. This order is rejected by al-Baghdadi. AFP Timeline: The emergence of Isis 2014 - January Isis fighters capture the Iraqi cities of Fallujah and Ramadi, giving them base to launch slew of attacks further south. AP Timeline: The emergence of Isis 2014 - June Isis declares itself the Caliphate, calling itself Islamic State (IS). The group captures Mosul, Iraq’s second largest city; Tal Afar, just 93 miles from Syrian border; and the central Iraqi city of Tikrit. These advances sent shockwaves around the world. Timeline: The emergence of Isis 2014 - June Around the same time Isis releases a video calling for western Muslims to join the Caliphate and fight, prompting new evaluations of extremists groups social media understanding. Timeline: The emergence of Isis 2014 - June Isis take Baiji oil fields in Iraq - giving them access to huge amounts of possible revenue. EPA Timeline: The emergence of Isis 2014 - August James Foley is executed by the group as concerns grow for second American prisoner, fellow reporter Steven Sotloff. AP Timeline: The emergence of Isis 2014 - August Obama authorises U.S. airstrikes in Iraq, helping to stall Isis’ along with action by Kurdish forces following the deaths of hundreds of Yazidi people on Mount Sinjar. Timeline: The emergence of Isis 2014 - September Isis release video showing Steven Sotloff’s murder prompting Western speculation his executioner is same man who killed Mr Foley. EPA Timeline: The emergence of Isis 2014 - September Obama tells us that America “will hunt down terrorists who threaten our country” EPA Timeline: The emergence of Isis 2014 - September Isis release a video appearing to show David Haines, who was captured by militants in Syria in 2013, wearing an orange jumpsuit and kneeling in the desert while he reads a pre-prepared script. It later shows what appears to be the aid worker's body. Rex Timeline: The emergence of Isis 2014 - September Peshmerga fighters scrabble to hold positions in the Diyala province (a gateway to Baghdad) as Isis fighters continue to advance on Iraqi capital. AFP Timeline: The emergence of Isis 2014 - October Aid worker Alan Henning is killed. Self-imposed media blackout refuses to show images of him in final moments, instead focuses upon humanitarian care. AP Timeline: The emergence of Isis 2014 - October Isis raise their flag in Kobani, which had been strongly defended by Kurdish troops. The victory goes against hopeful western analysis Isis had overextended itself, while alienating much of the Muslim population through the murder of Henning. Victory causes fresh waves of Kurdish refugees arriving in Turkey. Timeline: The emergence of Isis 2014 - November American hostage, who embarced values of Islam, Peter Kassig and 14 Syrian soldiers are shown meeting the same fate as other captives. But intelligence agencies will be poring over the apparently significant discrepancies between this and previous films. Seramedig.org.uk Timeline: The emergence of Isis 2015 - February Isis has released a video revealing the murder by burning to death of a Jordanian pilot held by the group since the end of December 2014. Reuters Timeline: The emergence of Isis 2015 - February Isis militants have released videos which appear to show the beheading of Japanese hostages Haruna Yukawa and Kenji Goto. Timeline: The emergence of Isis 2015 - February American aid worker, Kayla Mueller was the last American hostage known to be held by Isis. She died, according to her captors, in an airstrike by the Jordanian air force on the city of Raqqa in Syria, though US authorities disputed this. AP Timeline: The emergence of Isis 2015 - February Isis militants have posted a gruesome video online in which they force 21 Egyptian Coptic Christian hostages to kneel on a beach in Libya before beheading them. Egypt vowed to avenge the beheading and launched air strikes on Isis positions. AP Timeline: The emergence of Isis 2015 - February The British Isis militant suspected of appearing in videos showing the beheading of Western hostages has been named in reports as Mohammed Emwazi from London. Rex Features Timeline: The emergence of Isis 2015 - March Isis triple suicide attack has killed more than 100 worshippers and hundreds of others were injured after the group members targeted two mosques in the Yemeni capital of Sanaa. AP Timeline: The emergence of Isis 2015 - April Iraqi forces have claimed victory over Isis in battle for Tikrit and raised the flag in the city. EPA/STR Timeline: The emergence of Isis 2015 - April Isis has claimed responsibility for a suicide bomb attack in Afghanistan that killed at least 35 people queuing to collect their wages and injured 100 more. EPA Timeline: The emergence of Isis 2015 - April Isis’ media arm released a 29-minute video purporting to show militants executing Ethiopian Christians captives. The footage bore the extremist group’s al-Furqan media logo and showed the destruction of churches and desecration of religious symbols. A masked fighter made a statement threatening Christians who did not convert to Islam or pay a special tax. Timeline: The emergence of Isis 2015 - May Abu Bakr al-Baghdadi, the leader of Isis has been "incapacitated" by a spinal injuries sustained in a US air strike in Iraq. He is being treated in a hideout by two doctors from Isis’ stronghold of Mosul who are said to be "strong ideological supporters of the group". Timeline: The emergence of Isis 2015 - May Isis has also claimed responsibility for killing 300 of Yazidi captives, including women, children and elderly people in Iraq AP Timeline: The emergence of Isis 2015 - May Isis attack on Prophet Mohamed cartoon contest in Texas was its first action on US soil. Two gunmen were shot and killed after launching the attack at the exhibition. Elton Simpson and Nadir Soofi have been named as the attackers at the Curtis Culwell Centre arena in Garland. Timeline: The emergence of Isis 2015 - May Isis’s deputy leader, Abu Alaa Afri, a former physics teacher who was thought to have taken charge of the deadly terrorist group, has been killed in a US-led coalition airstrike. Timeline: The emergence of Isis 2015 - May US special forces have killed a senior Isis leader named as Abu Sayyaf in an operation aiming to capture him and his wife in Syria. Getty Images Timeline: The emergence of Isis 2015 - May Iran-backed militias are sent to Ramadi by the Iraqi government to fight Isis militants who completed their capture of the city. Government soldiers and civilians were reportedly massacred by extremists as they took control and the army fled. Charred bodies were left littering the city streets as troops clung on to trucks speeding away from the city. Ramadi is the latest government stronghold to fall to the so-called Islamic State, despite air strikes by a US-led international coalition aiming to stop its advance in Iraq and Syria. AFP Timeline: The emergence of Isis 2015 - May Isis rounded up civilians trapped in Palmyra and forced them to watch 20 people being executed in the historic city’s ancient amphitheatre. The Unesco World Heritage site was overrun by militants, threatening the future of 2,000 year-old monuments and ruins. Thousands of Palmyra’s residents fled but many are still living within the city walls, while the UN human rights office in Geneva said it had received reports of Syrian government forces preventing people from leaving until they retreated from the city. Getty Timeline: The emergence of Isis 2015 - May A group of Isis-affiliated fighters have captured a key airport in central Libya. The militants took control of the al-Qardabiya airbase in Sirte after a local militia tasked with defending the facility withdrew from their positions. Affiliates of Isis, already control large parts of Sirte, the birthplace of former Libyan leader Muammar Gaddafi and a former stronghold of his supporters. Timeline: The emergence of Isis 2015 - June The US Air Force has destroyed an Isis stronghold after an extremist let slip their location on social media. According the Air Force Times, General Herbert "Hawk" Carlisle, commander of Air Combat Command, said that Airmen at Hulburt Field, Florida, used images shared by jihadists to track the location of their headquarters before destroying it in an airstrike. Reuters Timeline: The emergence of Isis 2015 - June Kurdish forces captured a key military base in a significant victory in Raqqa as well as town of Tell Abyad. YPG fighters, backed by US-led airstrikes and other rebels, consolidated their gains, when they seized the key town on the Syria-Turkey border. They are now just 30 miles to the north of Raqqa and have cut off a major supply route deep inside Isis-held territory. Ahmet Silk/Getty Timeline: The emergence of Isis 2015 - June Isis has released gruesome footage claiming to show the murder of more than a dozen men by drowning, decapitation and using a rocket-propelled grenade as it seeks to boost morale among its fanatical supporters. Timeline: The emergence of Isis 2015 - June Isis has begun carrying out its threat to destroy structures in the ancient Syrian city of Palmyra, blowing up at least two monuments at the Unesco-protected site as Syrian government troops made advances on the Islamist’s positions. AFP

"They took our money, documents and mobile phones and sent us home," she says. "After 13 days they knocked on our door and the men were separated from the women. Thirty women were taken with their children to one house and told they must convert to Islam, pay a tax or be killed. We told them that since they had taken all our money, we could not pay them." Four days later, some fighters burst into the house saying they would kill the women and the children if they did not convert.

Soon afterwards, Mrs Matti was taken to Mosul in a car with three other women and a guard who, she recalls, threw a grenade into a house on the way to frighten them. In Mosul they were taken first to al-Kindi prison, formerly an army camp, but did not enter it and then their guard got a phone call to bring them to a house in the Habba district of the city.

The Matti family

In the house, she and the three other Christian women were put in one room, next to another in which there were 30 Yazidi girls between 10 and 18 who were being repeatedly raped by the guards. Mrs Matti says that "the Yazidi girls were so young that I worried about Nevin and told the guards that she was eight years old though she is really 10".

They told her that her husband, Adel, had converted to Islam. She asked to speak to him on the phone, saying she would do whatever he did. They spoke, and agreed that they had no choice but to convert if they wanted to survive.

When they appeared before an Islamic court in Mosul to register their conversion, their three children were given new, Islamic names: Aisha, Abdel-Rahman and Mohammed. They went to live in a house in a Sunni Muslim district and from there – here the husband and wife are circumspect about what exactly happened – they secured a phone and contacted relatives in Irbil. They said that they needed to take one of their children for medical treatment in Mosul city centre, and, once there, they had a pre-arranged meeting with a driver who took them by a roundabout route through Kirkuk to the protection of the KRG.

The trauma of the last six months has been overwhelming for the remaining Christians in Iraq. The Chaldean Archbishop of Irbil, Bashar Warda, heads an episcopal commission to help displaced Christians whom he says number 125,000, or half the total remaining Christian population. Unlike other displaced people in Iraq, the Christians are mostly cared for by the churches. He says that there will always be a few Christians remaining in Iraq, but overall "they have lost their trust in the land. Some 80 or 90 are leaving every day for Turkey, Lebanon and Jordan." Others would go if they had money and visas.

Mounting persecution since 2003 and now the final calamity of Isis taking Mosul and the Nineveh Plain has convinced many that they can no longer stay. The archbishop suspects that, even if IS is driven back and Christians can return to their homes, half of them will only stay long enough to sell their property. Almost exactly a hundred years after the Armenian Christians in Turkey were slaughtered or driven into exile, the end has come for the Christian community of Iraq. "Have no doubt," concludes Archbishop Warda, "that here is massacre, here is a tragedy."

Iraq’s Christian heritage

The Christian communities in Iraq can trace their history back to the early days of their faith. Most are Chaldeans, a small sect which is autonomous from Rome but which recognises the authority of the Pope. There are an estimated 500,000 ethnic Assyrians indigenous to northern Iraq, south-east Turkey, north-east Syria and north-west Iran. This group is so ancient that some of its members still speak Aramaic, the language of the New Testament.

The country’s other major Christian community is also Assyrian, and its Ancient Church of the East, having embraced Christianity in the first century AD, is believed to be the oldest Christian denomination in Iraq.

In addition to these groups, there are small communities of Syrian Catholics, Armenian Orthodox and Armenian Catholic Christians, as well as Greek Orthodox and Greek Catholic communities.