Whoever said “A week is a long time in politics” has not faced the new levels of uncertainty of the Syrian uprising. This week U.S. Secretary of State John Kerry, in an effort to resolve the Syrian crisis, insisted that Bashar al-Assad could not be part of a future transitional government. This poses the question, if the dictator Bashar al-Assad is deposed, who or rather what faction would take his place?

In March, President Obama warned that “extremists thrive in chaos” as he resisted calls from U.S. lawmakers to get involved, deepening the crisis of the Syrian uprising. The president delivered a grave warning on his tour of the Middle East about the danger of post-Assad Syria becoming a haven for Salafist extremists, many having ties with al-Qaeda.

He portrayed a nightmare scenario in which Syrian institutions were destroyed beyond recognition and the country divided by sectarianism, with jihadists filling the gap.

“Something has been broken in Syria, and it’s not going to be put back together perfectly immediately, even after Assad leaves,” Obama said. “But we can begin the process of moving it in a better direction, and having a cohesive opposition is critical to that.”

Opposing Assad’s army are two rebel forces: the Free Syrian Army and Jabhat al-Nusra, a jihadist group that recently declared its allegiance to al-Qaeda. Known for their fighting prowess honed in Iraq, al-Nusra are now taking the lead in nearly every front line in the Syrian war.

As al-Nusra forces gain more territory through military bombings and suicide bombings in heavily populated areas where ordinary civilians try to survive this civil war, they have attracted worldwide criticism. U.N. human rights investigators have gathered testimony from casualties of Syria’s civil war and medical staff indicating that rebel forces may have used the nerve agent, sarin.

With the emergence of recent reports of the use of sarin gas in this warfare and continual escalation of fighting in Damascus and on the borders of Jordan, Lebanon and Iraq — as well as the 500,000 refugees fleeing the conflict — the Syrian uprising could potentially spill over to other regions in the Middle East, destabilizing a region already fragile from post-Arab Spring uprisings.

Spillover could destabilize region

In the runup to Obama’s Middle Eastern tour, foreign policy analysts in Washington warned about Syria turning into a failed state. One adviser said “…about half the country’s economy had collapsed since fighting began. If Syria became a power vacuum in which jihadists could operate freely, this could pose a threat not only to Israel but to neighboring countries such as Jordan and Lebanon.”

In an effort to contain the Syrian conflict within its own border, Jordan has progressively moved to arm the Free Syrian Army (FSA) as an attempt to stop al-Qaeda advances into Jordan while at the same time attempting to stabilize the Syria conflict.

For the last two months, Jordan has initiated a policy to arm rebel groups on its borders of southern Syria. In reports by the Guardian, it is believed that Saudi Arabia has backed Jordan by giving 1 billion U.S. dollars.

This is a significant change of direction for Jordan ministers, from a policy of trying to contain the spillover threat posed by the civil war across its border to one of actively choosing a rebel faction to try and end the war before it engulfs the cash-strapped kingdom.

It is only recently that King Abdullah has actively sought some resolution to the Syrian uprising. In the past he has been reluctant to take direct action against Syria, only opting to open Jordan’s borders to refugees and defectors, but neither allow them to be used for gun-running nor to interfere or topple the four-decade Assad dynasty.

According to the Guardian, Jordanian and Western sources say Abdullah’s calculation is that the sooner the Syrian crisis is over and more moderate elements are able to defeat Assad, the better the chances are of a moderate regime taking over in Damascus. “It’s a race between [al-Qaeda affiliate Jabhat al-Nusra] and the regular rebels to Damascus,” said one Western official. “And it’s in no one’s interests if al-Qaeda wins.”

Recently, Jabhat al-Nusra, the al-Qaeda-linked group at the vanguard of much of the fighting in north and east Syria, renewed a pledge of allegiance to al-Qaida’s overall leader, Ayman al-Zawahiri. A day earlier, al-Qaeda groups who have used Iraq as a base since the U.S. invasion and the deposing of Saddam Hussein, claimed it was formally allied with al-Nusra.

The Syrian opposition’s civilian body said that it was “deeply concerned” about the Jabhat al-Nusra statement. “The Syrian coalition urges Jabhat al-Nusra to stay within the ranks of nationalistic Syrians, to continue its efforts in fighting the Assad regime, and in supporting and protecting the freedom of all Syrian sects,” it said.

Civilians have paid a heavy price in this conflict, with more than 70,000 people killed in the war, and reports for human rights groups saying that there are 3 million Syrians who have been forced to flee their homes.

Displaced, hungry and sometimes injured or pregnant, Syrians have traveled to refugee camps in Turkey and Jordan as the ongoing violence threatens their homes.

Role of the West is unclear

Britain and French governments had been accused of “directly or indirectly” supporting al-Qaeda in an escalating war against Syria. Faisal al-Miqdad, Syria’s vice-foreign minister, used a rare interview to attack the U.K. and France as “new colonialists” for providing political and military support to opposition fighters seeking to overthrow the president, Bashar al-Assad.

At the EU summit in April, both Britain and France raised the pressure on other EU members to lift a ban on supplying arms to Syria. Britain warned that it could break with the embargo altogether, which requires unanimous agreement by the EU’s 27 members to take effect, while France hinted it would push to get the bloc to agree to amend the ban to allow the supply of arms.

Evidence of the growing strength of al-Nusra, gathered from Guardian interviews with FSA commanders across Syria, underlines the dilemma for the U.S., Britain and other governments as they ponder the question of arming anti-Assad rebels.

John Kerry, the U.S. secretary of state, said that if negotiations went ahead between the Syrian government and the opposition – as the U.S. and Russia proposed last Tuesday – “then hopefully [arming the Syrian rebels] would not be necessary.”

The agreement between Washington and Moscow creates a problem for the U.K. and France, which have proposed lifting or amending the EU arms embargo on Syria to help anti-Assad forces. Last Tuesday, John Kerry brokered a deal with Russia pushing for an international conference aimed at ending the civil war in Syria, through new diplomatic pressures.

The British Foreign Office welcomed the agreement as a “potential step forward” but insisted that “Assad and his close associates have lost all legitimacy. They have no place in the future of Syria.” Opposition leaders were skeptical about prospects for talks if Assad remained in power.

Illustrating their plight, FSA commanders say that entire units have defected and joined al-Nusra while others have lost a quarter or more of their strength to them recently.

“Fighters feel proud to join al-Nusra because that means power and influence,” said Abu Ahmed, a former teacher from Deir Hafer who now commands an FSA brigade in the countryside near Aleppo. “Al-Nusra fighters rarely withdraw for shortage of ammunition or fighters and they leave their target only after liberating it,” he added. “They compete to carry out martyrdom [suicide] operations.”

Abu Ahmed and others say the FSA has lost fighters to al-Nusra in Aleppo, Hama, Idlib and Deir al-Zor and the Damascus region. Ala’a al-Basha, commander of the Sayyida Aisha brigade, warned the FSA chief of staff, General Salim Idriss, about the issue last month. Basha said 3,000 FSA men have joined al-Nusra in the last few months, mainly because of a lack of weapons and ammunition. FSA fighters in the Banias area were threatening to leave because they did not have the firepower to stop the massacre in Bayda, he said.