Fighters of the Islamic State of Iraq and the Levant stand guard at a checkpoint in the northern Iraq city of Mosul. - Reuters

The official story is that northern Iraq is at peace. The Islamic State of Iraq and the Levant (Isil) has largely been defeated; the Iraqi Army and its allies are in charge. But for Christians, the persecution continues.

Those who can are getting out. Those who stay are preparing themselves for more violence. "Things are bad more than any other time," Fr Behnam Benoka tells me at his church in Bartella, a ghost town protected, if that's the right word, by soldiers with Kalashnikovs. "It's harder even than before Isil."

Isil was a nightmare, the worst one can possibly imagine. But Christians say that having left their homes to escape Sunni fundamentalism, they've returned to find their lands are now dominated by Shia militia sponsored, allegedly, by Iran. Christianity, they fear, faces extinction in what was once a multicultural society.

My guide on this trip is Fr Benedict Kiely, an English priest who runs a charity called Nasarean.org that provides advocacy and aid for Iraqi Christians. He knows a man who knows a man who gets us through countless checkpoints, themselves a brazen display of the contest to control the region known as the Nineveh Plains.

Nineveh lies north and east of Mosul, traditionally regarded as home to the tomb of the prophet Jonah; so old is the Christian community here that the men in our car speak conversational Aramaic, the language of Jesus.

Grafitti on Our Lady cathedral, Mosul, Iraq, reads "Entry forbidden upon the order of the Islamic state" Credit: Tim Stanley

Under Saddam Hussein Christians enjoyed relative tolerance and stability. Many were middle-class and some held positions in the ruling Baath Party, all of which would later make them a target for retribution. It’s estimated that the Christian population has fallen from around 1.5 million under Saddam to about 250,000 today, a decline that began under the dictator. In the late Nineties, Saddam found god in a bid for legitimacy. Islamic religious education was encouraged and young radicals went to Saudi Arabia for instruction.

In the car, Yohanna Towaya, a Christian who previously lived and worked in Mosul as a professor, divides history into “before 2003 and after 2003.” The West invaded in March of that year. In September, he recalls, the Islamic mullahs in Mosul began to preach that “the Christians are infidels and also aiding the Americans.” Islamists took effective control, sponsored, he says, by al-Qaeda.

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They kidnapped Christians, ostensibly to raise cash for the anti-American resistance. Mr Towaya’s own brother and brother-in-law were taken while working in the fields: men approached them with guns and said “come with us”. Mr Towaya shrugs: “This was ordinary.” The kidnappers set their ransom at $500,000, an absurd sum, but the Towayas knew a general who was able to negotiate the men’s release. If anyone couldn’t pay, the victim was beheaded and their body dumped in the street.

Mr Towaya says that between 2003 and 2014, “The majority [of Christians] left Mosul and went to the [surrounding] Nineveh plains”. Some fled abroad, to Lebanon, Jordan, Turkey, even Syria. His own family returned to their ancestral home in Qaraqosh on the Plains. But something even worse was coming. On June 10, Isil - an army of Sunni Jihadists Hell-bent on building a new empire - captured Mosul.

Mr Towaya explains: “On the first day, they didn’t say anything about Christians. Christians were very comfortable in the first week. But after 15 days, they asked Christians to leave town. They must leave, or convert, or be killed.” On August 6, Isil expanded into the Nineveh Plains, including Mr Towaya’s town. Mr Towaya and an estimated 125,000 Christians took to the road and drove east, to Kurdistan. Overnight, the Kurdish city of Erbil became a giant camp. Refugees slept on building sites or in the streets.

As for what happened in occupied Mosul, one can see with one’s own eyes. At noon, a man walks through the traffic in a daze; he is missing both arms. That was one of the ways Isil dispensed its justice.

The eastern half of Mosul is recovering from the war but the western, older and more Christian part is still a wasteland. Isil went on an orgy of destruction, including blowing up the famous leaning minaret at the al-Nuri mosque, where Abu Bakr al-Baghdadi declared the foundation of the Isil caliphate. Its green dome still stands, just, in a field of bricks and concrete. There are likely still to be bodies underneath. Amazingly, human beings live among the ruins. The first few shops to return were barbers and men’s clothes. Iraqi men like to look good. I see almost no women.

The toppled remains for the Al-Tahira Church in Mosul Credit: Tim Stanley

The courtyard of the Syriac cathedral doubled as a firing range. The dome of the Chaldean Al-Tāhirā church, which dates from the 18th century, was blown off the tower and landed upside down on the roof; it sits there like a giant spinning top. On the walls of the cathedral of Our Lady is written in Arabic: “Entry forbidden on the orders of the Islamic State.” Climbing the stairs, past rooms with no floors, I discover a scattered pile of Christian instructional books; a sign of how fast people had to flee and, given that they’re still lying there, that hardly anyone has been back since. No wonder. Isil had a very special purpose for churches. It turned them into torture chambers. From the top of Our Lady, Fr Benedict points to a bell tower. That’s where they hanged people.

Not everyone got out. We drive to a Kurdish suburb to meet a Christian family who stayed in Mosul during the occupation and, in order to survive, publicly converted to Islam. They bear the classic signs of trauma: they joke, they scream, they shout. After an impassioned argument - as much with himself as anyone else – the son tells his story. He speaks in a detached monotone, as if recalling something that happened to someone else. I agree to withhold his name.

He says: “When Isil conquered Mosul they were as angels. They said they came to save us from injustices. The people who left before because of danger came back: Isil gave aid to the people. They had their laws and their propaganda and they punished people [but] they had an administration and it gave order. All the Christians who stayed converted and they liked it” - at first.

Under Isil, conversion to Sunni Islam was mandated: he was told either his family should do it or they would all be killed. So, they did. They had to submit to the new laws of the city, which were enforced by a religious police force. “All are forced to go to the prayers. If [the religious police] see someone in the street, not in the mosque, they will punish you. If you are three minutes late, they punish you.”

Men had to wear beards and were forbidden from smoking; the religious police would sniff their fingers to see if they’d obeyed the commandment. Women were told never to go out unaccompanied by a male relative. They had to wear the head-to-toe niqab, including gloves. If the religious police saw an exposed finger, they would bite it.

Many women had never before worn the niqab and they kept falling over in the street. If a man who wasn’t a relation helped them up, he’d be punished. Television was banned. I ask if the city was quiet. He shakes his head. “All the time there is explosions and drone strikes. All the time there is shooting.” There were foreigners among Isil: he saw a Chinese fighter.

ISIL fighters celebrate on vehicles taken from Iraqi security forces in Mosul in 2014 Credit: Reuters

It seems that Isil did take the family’s conversion at face value but “sometimes they asked you about religion and if you couldn’t answer, they punish.” What exactly did he mean by “punish?” It was a trial without witnesses or lawyers. Those found guilty were taken to a spot opposite the market and that’s where Isil would “cut their hands and head off. They would gather all the people with loudspeakers to see and to hear.” He was present at an execution by defenestration. “At 4pm… we see people gathering. They brought someone from a car and took him up to the third floor and threw him off. He died.” His executioners then “came out [of the building] and threw stones at him.” They stoned a dead body.

In October 2016, the Iraq Army and Shia militia liberated Mosul from Isil, along with the Nineveh Plains. This family, now free to leave Mosul, went to a refugee camp. They now have to live with the stigma of having converted.

Mr Towaya returned to Qaraqosh to find that his brother’s house, next door to his own, was missing: evaporated by a bomb. Mr Towaya’s house had been occupied by Isil. There was a pile of books and clothes lying on the floor waiting to be burned but, he assumes, the Jihadists took fright and ran before they could light it. Almost no one went back to Mosul. Fr Benedict says he was the first Western priest to have visited the city, very shortly after liberation. The bodies had been removed but detritus remained. “We saw sludge, literally sludge where a body had lain days before. That and beard hair”, so much of it he thought at first that he was looking at carpet. Isil fighters shaved their beards off before slipping away into the villages and rural population.

They’re not entirely gone: this week, the Iraqi military announced a sweep of the countryside to dig out Isil cells. But even if Isil’s local power base is lost, even if there is no hunger for the return of the caliphate in Mosul, there are signs that Sunni fundamentalism is being replaced by Shia chauvinism with long-term objectives. In the course of this mass movement of people across northern Iraq, the Christian population fell but the concentration of Shabak Arabs grew, a mostly Shia ethnic group boosted by the pro-Iran Shia militia. In the view of Fr Benoka, a new coalition of interests “want to force [the Christians] from our lands.”

Fr Benoka in his rebuilt church in Bartella, Nineveh Province

Politics and civil society are in pieces; the armed forces are in control of the Plains. They harass citizens and they are turning the screws on business and culture. It’s become expensive to lease shop space in Nineveh, which rules impoverished Christians out of the marketplace, and those who do run a store, says Fr Benoka, are targets of a covert boycott. “All the Muslims have orders: do not buy from Christians.”

In Bartella itself, the Shia “put their loudspeakers on top of the public library”, direct them at the Christian areas, and “start broadcasting their prayers all day, starting at 4.30 am… They are also putting Shia religious monuments [in front of] our Christian historical sites” to dwarf them and reclaim the landscape. This I saw for my own eyes: on the road in front of the town now stands a large portrait of the Shia hero Ali, with his famous lion. The Shia militias can accurately say “We are not killing Christians,” complains Fr Benoka, but “what kind of life can a Christian lead?” The priest estimates there were around 85,000 Christians living in Nineveh’s towns before Isil; he thinks there is probably less than a third left. If there is a war between the United States and Iran, the region could be a battlefront.

The young and educated are getting out fast, although not to Britain or America. Iraqi Christians report that the UK isn't handing out visas, while the number of Christian refugees admitted to America has fallen by 98 per cent in two years under Donald Trump. The Trump administration prefers to focus resources on making life better on the Plain: they are paying to remove rubble and on every street corner of Qaraqosh is a garbage can donated by Washington. Yet Nineveh is being ethnically cleansed – not just by the violence of Jihadis but, under this fragile peace, by poverty and insecurity.

I meet with Archbishop Bashar Warda at his cathedral in Erbil, which was once packed with refugees. He recently told a British audience that his people face “extinction”. With me he calculates that “the situation is very vulnerable” and the West is not doing enough. Iraq’s Christians need jobs and investment, yes, but they also need the West to recognise honestly what is happening. I explain that some Western governments like to think of themselves as “colour blind” – as favouring neither one religious group nor another, and especially not Christianity, which they see as Western and privileged. The Bishop is appalled: “Christians have been targeted, persecuted, so you have to help them.” If the West’s policy is to aid anyone who is suffering – in an objective fashion – then necessity dictates they help the Christians because “it happens to be Christians this time.”

Is Britain saying “we can’t help you because you are Christian?” he asks. “That is a type of discrimination. You help those who need help. That is the criteria.”