Amman — Beirut — Istanbul

I recently bumped into a senior officer with the rebel Free Syrian Army who was waiting in the passport queue at the Turkish border. I didn’t recognise him at first, out of uniform and without his entourage, and I told him so. He was following the example of the 7th-century Second Caliph, Omar bin al Khattab, he replied. The caliph was so humble he took turns with his servant riding a horse to Jerusalem to receive the city’s surrender.

There was no imagery from Islamic history when I first met the officer a year ago. He was one of those ‘rebels’ western officials have in mind when they describe a ‘secular, moderate’ armed opposition. But more and more, rebels pepper their conversation with quotations from the Koran. With their lives on the line, perhaps people are turning to God. Perhaps, with the jihadis in the ascendant, such talk is politic. Later, the officer appeared on YouTube next to a notoriously bloodthirsty Chechen commander. ‘We kiss the hand that holds the trigger against Assad,’ he said.

It should not have been a surprise, therefore, when last week several FSA brigades issued ‘Communiqué No. 1’ announcing an alliance with the Nusra Front, al-Qa’eda’s Syrian subsidiary. The communiqué rejected the Syrian National Coalition, the SNC, the body promoted by London and Washington as the ‘sole legitimate representative’ of the Syrian people. It gave voice to the fighters’ deep and long-held contempt for the SNC’s exiled politicians, who have spent the past two years squabbling in five-star hotels as Syria burned. ‘If any of them come here,’ a rebel commander told me, ‘I will hang them.’

Most importantly, Communiqué No. 1 says the rebels are fighting not for democracy, but for Sharia, ‘the sole source of legislation’. It was signed by what is probably the FSA’s biggest brigade, with thousands of men, Tawheed, or ‘one God’. Its leader, Haji Marea, is the FSA’s commander for northern Syria. Balding, in his thirties, and with a mild manner that belies his reputation for bravery, he told me he was a ‘moderate Islamist’. ‘We stand for a tolerant Sharia, one that gives proper rights to all threads of the Syrian social fabric,’ he said.

Haji Marea sits on the FSA’s Supreme Military Council, the National Coalition’s military wing, also backed by western governments. It is not clear if he thinks he can remain on the council but in a sense that doesn’t matter. The FSA that London and Washington speak to has been revealed as a reassuring fiction, irrelevant to the real alliances on the ground, where most fighters believe they are waging a religious war. As well as the pact with the Nusra Front, Haji Marea has friendly relations with an even more extreme al-Qa’eda group, the Islamic State in Iraq and Syria, Isis. ‘Anybody against the regime is our ally,’ he said. ‘And Isis is fighting the regime.’

Everyone in rebel-held areas will tell you that the Islamists, of whichever stripe, are making gains because of the ‘secular’ FSA’s corruption and opportunism. That and the fact that most of the money and guns are going to the Islamists, sent by Qatar and Saudi Arabia. ‘Ali’ had been a flight attendant with Emirates before the war, living in Dubai and going to bars to pick up girls. Now he was in a Nusra Front brigade, he told me, but only because he thought they were really taking the battle to the regime. The emir of his group had banned smoking in line with Islamist doctrine. Ali would sneak outside for a crafty cigarette. He wasn’t an Islamist, he said, he just wanted Assad gone.

The bits of the FSA that continue to oppose Nusra and the Islamic State blame the West for their loss of power. ‘The Syrian people will welcome any support if the West continues to abandon us,’ the FSA’s commander for southern Syria, Abu Fadi, told me in Jordan. Abu Fadi said that, contrary to reports in the US newspapers, he had received almost no American help. None of his men had been trained in the camps that supposedly exist in Jordan. No weapons had been handed over. ‘We have had some new boots and jackets,’ he said with a snort. ‘That’s all.’

Isis and their satellites are still far from a majority but they have influence beyond their numbers. Public beheadings are now common in northern Syria. The BBC obtained pictures of one, the executioner dressed in black waving a severed head before a jubilant crowd.

Amid what the guidebooks call the ‘stylish and opulent’ surroundings of the Albergo hotel in Beirut, a western diplomat was briefing journalists. The room was all Persian rugs and wing-backed chairs. Waiters hovered. The official was his government’s main conduit to the Syrian rebels. I asked him what percentage of the rebels western countries could support: what percentage were not jihadis, not committing human rights abuses, looting or kidnapping — and were militarily effective?

There was a silence. Finally, he said: ‘Thirty per cent.’ It was a devastating admission. Then he paused and said he had been considering only the first three criteria. Adding in military effectiveness, you would have to say the West could support only 10 per cent.

Western diplomats are now scrambling to ensure that 10 per cent has at least the appearance of running the show. One official denied that Communiqué No. 1 represented an end to western illusions. ‘Any attempt to impose an authoritarian Islamist system on Syria by force will not lead to peace,’ he said. ‘Quite the reverse. And it will be rejected by the vast majority of Syrians.’

But parts of northern Syria are already an Islamic emirate in the making. All of the opposition-held areas are contested by shifting alliances of competing rebel groups, mostly Islamist in character. There are 1,200 armed groups, according to one estimate. Who is in charge varies not just from town to town, but from one street corner to the next. It is ‘Somalia on the Mediterranean’.

Is the Islamist alliance the end of the FSA — and the evisceration of western policy — that it seems to be? If so, there is one tiny shaft of light for western governments. The Islamist groups who signed the declaration, even the Nusra Front, say they are waging a holy war — but only in Syria: it is not a global jihad. That might be taken as an argument to support the moderate Islamists against the jihadists who want to use Syria as a base to export violence. Or it might be an argument to stay out of Syria altogether. Regardless, the regime now has the enemy it wants. And President Assad is looking stronger than ever.