Once again high noon seems to be beckoning for Syria and its beleaguered civilian population.

Later this week, members of the UN Security Council will debate a fresh resolution – drafted by Britain – which will threaten the regime of President Bashar al-Assad with fresh sanctions unless it accepts a transition plan including new elections. And once again when it is debated the move will most likely founder under Russia and China vetoing it.

With the current UN mandate set to expire on Friday, it looks as though the violence will continue and that the world will have to look on helplessly as Syrian security forces indulge themselves in the kind of massacre that killed 200 people in Hama province last week. In a grim way it looks like business as usual – except there has been a step-change in the way the conflict is being fought.

There is growing evidence that the fighting is involving Muslim fundamentalists from across the Arab world, and that their influence could have a greater effect on unseating Assad than any fresh UN resolution. For some time it has been clear that al-Qaeda fighters have been engaged in the increasingly bitter conflict and that their involvement is predicated on the imposition of sharia law and the creation of an Islamic republic.

Last week in the northern Syrian province of Idlib, black al-Qaeda flags were seen flying in some of the fighting units of the Free Syrian Army (FSA), which is spearheading the struggle against Syrian security forces.

Western intelligence services monitoring the fighting now accept that fundamentalists will influence the eventual outcome. Even if the fighters are not actual members of al-Qaeda, they support its ideology and use it as a rallying point in the battle to unseat the president. As happened in the recent civil war in Iraq, which quickly degenerated into a struggle between rival religious groups, al-Qaeda is less of a military grouping and more of an ideological franchise.

Destroying the secular rule of Assad, right, has become a stated aim in the Syrian conflict and the call has provided the FSA with an impetus which is similar to the arrival of modern weapons supplied by friendly countries including Saudi Arabia and Qatar. The war in Syria was always in danger of becoming a civil conflict. Now it will be fought on religious grounds, turning the country into the kind of battleground that neighbouring Lebanon became quarter of a century ago.

Those claims have been reinforced by evidence that last week's massacre was perpetrated not by regular soldiers of Assad's army but by Shia militias loyal to – but not necessarily controlled by – his government. With evidence mounting of the involvement of jihadist fighters, many of the militias see it as their religious duty to crack down on the largely Sunni population which has already born the brunt of government repression.

Against that background, the UN is increasingly powerless to prevent further acts of violence. Although some sanctions have been imposed, the lack of a united front means that they can be easily flouted. Some of the weapons being used by the Syrian army are clearly Russian, notably the helicopter gunships and armoured vehicles which took part in operations against the civilian population last week.

The one hope for a cessation of hostilities is that Assad's government might implode, just as the Libyan regime did in the dying days of the insurrection against Muammar al-Gaddafi last year. The unexpected defection last week of a leading Syrian diplomat raised the tempo of optimism – Syria's former ambassador to Iraq fled to Qatar and called on all Syrians to "join the ranks of the revolution" and turn their guns on the Assad regime. For the FSA it was a major propaganda coup, but it will need to be followed by other senior defections to have any real effect on the direction of the war.

Yesterday, UN Secretary-General Ban Ki-Moon warned that the war in Syria was spiralling out of control and that the world could not afford to sit by and watch. But despite that impassioned plea, and after almost 18 months of massacre and reprisals, the UN is still powerless to introduce measures to stop the violence.

With time rapidly running out, the upshot will be decided not by words uttered by the diplomats at the UN but by whichever side gains military superiority in the killing grounds of the Syrian countryside.