The Obama Administration has been calling for the removal of President Assad’s regime almost from the beginning of the conflict. Regime change in Syria was a serious consideration for the Bush Administration. It was one of several countries in the region on President Bush’s hit list after an anticipated quick victory quick victory in Iraq.

The U.S. has always objected to the fact that Syria has been close to Russia and the USSR since the 1950s though Damascus and Moscow have had sharp differences at times. The two countries cooperate in military, trade and economic matters. (Russia’s only naval base in the Mediterranean is in Syria’s port city of Tartus.) Both countries have long been critics of U.S. hegemony and Israel’s maltreatment of the Palestinians. As if this weren’t enough, the Syrian government enjoys warm relations with Iran — a coupling some Israeli leaders identify as an “Axis of Terror.”

Obama may want Assad out, but more than that, he doesn’t want the jihadists in, which helps explain Washington’s reluctance to seriously intervene until it can create a united Syrian front subordinate to U.S. interests that can handle the political and military aspects of regime change in Damascus, including a successor to Assad.

The White House has spent the last two years molding the Syrian National Council (SNC) and “moderate” elements of the Free Syrian Army (FSA) to lead the revolt. But the SNC, mainly composed of Syrian exiles, is frequently squabbling and has lost considerable support within the country. The FSA is said to be entirely composed of Sunni Muslims who are fighting against the largely Alawite government leadership in Damascus. The Alawites are an offshoot of the Shia branch of Islam. The jihadists are far less interested in democracy than in removing the “ungodly” Shi’ites from power.

In the face of reports that jihadist groups were increasing their strength within the oppositionist armed forces, Secretary of State Kerry asserted recently that moderate Syrian opposition groups are growing in influence. Responding to a comment made at a Senate Foreign Relations committee meeting Sept. 6 Kerry declared: “I just don’t agree that a majority [of opposition forces] are al Qaeda and the bad guys. That’s not true. There are about 70,000 to 100,000 oppositionists… Maybe 15% to 25% might be in one group or another who are what we would deem to be bad guys.”

Nearly a thousand armed groups, most relatively small, are engaged in fighting against the Syrian government, but not all follow the designated FSA leadership. The fighters fall roughly into three groups — nationalist secularists (including many former Syrian soldiers who joined the opposition and who are backed by the U.S.), nationalist jihadists (primarily the Muslim Brotherhood) and international jihadists. “International” pertains to (largely Salifist) groups such as al-Qaeda that extend the fight for Sunni Islamic supremacy to all Muslem countries, not in just a single state.

Martin Chulov (Guardian UK May 30) reported: “The al-Qaeda-aligned groups that started mustering in Syria from July 2012 onwards have been consolidating in large swaths of the north and east and spreading out…. Black flags now fly above many mosques and civic buildings in towns across Syria’s north…. and in Iraq’s border towns.”

Various reports now indicate that jihadist elements are large and swiftly growing. The conservative Economist declared Sept. 28: “The prospect of overthrowing Bashar Assad is catnip to jihadists; his Alawite regime is an heretical abomination to the hyper-orthodox Salafism from which al-Qaeda draws its support. Western intelligence thinks most of Syria’s effective rebel militias may now be jihadist, with thousands of fighters from other Muslim countries and hundreds from Europe, especially Britain, France and the Netherlands…. The Islamic State of Iraq and al-Sham (ISIS), related to al-Qaeda in Iraq (AQI), has recently pushed into eastern Syria from Iraq, following a resurgence there.” (Regarding ISIS and the connection to Iraq, see article below, “Iraq’s Undeclared War.”)

On Sept. 25 Reuters reported:  “A group of powerful rebel units have rejected the authority of the Western-backed Syrian opposition leadership abroad and called for it to be reorganized under an Islamic framework, according to a video statement posted on the internet. At least 13 rebel factions were said to have endorsed the statement, including the al-Qaeda-linked Jabhat al-Nusra (Nusra Front) and the powerful Islamist battalions Ahrar Asham and the Tawheed Brigade.” ISIS was not among them because of hostility and rivalry between that organization and the al-Nusra.

These groups represent tens of thousands of fighters. Radio Free Europe/Radio Liberty speculated that “if the coalition holds, it could mean Western powers would have no influence over what happens on the ground over a large part of the north as well as parts of Homs and Damascus.”

The Wall Street Journal reported Sept. 18: “In recent months, ISIS has become a magnet for foreign jihadists who view the war in Syria not primarily as a means to overthrow the Assad regime but rather as a historic battleground for a larger Sunni holy war. According to centuries-old Islamic prophecy they espouse, they must establish an Islamic state in Syria as a step to achieving a global one…. The proliferation of the Sunni jihadists and extremists has brought a new type of terror to the lives of many Syrians who have endured civil war in the north. Summary executions of Alawites and Shiites, who are seen as apostates, attacks on Shiite shrines, and kidnappings and assassinations of pro-Western rebels are on the rise.”

The daily Telegraph (UK) reported Sept. 12: “A new study by IHS Jane’s, a defense consultancy, estimates there are around 10,000 jihadists [in Syria] — who would include foreign fighters — fighting for powerful factions linked to al-Qaeda. Another 30,000 to 35,000 are hardline Islamists who share much of the outlook of the jihadists, but are focused purely on the Syrian war rather than a wider international struggle. There are also at least a further 30,000 moderates belonging to groups that have an Islamic character, meaning only a small minority of the rebels are linked to secular or purely nationalist groups.”

The Syrian rebels have considerable material support from Saudi Arabia, Qatar, and lesser from Turkey and the U.S. Much of NATO, Israel and many of Washington’s allies back the rebels as well. Russia and China back Syria in the UN. Russia also supports the Assad government with weapons. Iran also offers support, as does Hezbollah, the Shia self-defense organization in Lebanon that has sent fighters to Syria.

Secularists in the FSA are obviously worried about the rise in jihadist strength. The Damascus regime is said to welcome negotiations to end the war, which appears to have become stalemated. The opposition has rejected negotiations before, demanding that Assad first step down.

Assad has let it be known that he intends to remain in office and that he has the right to decide whether to run for reelection next year.

Stratfor’s Friedman argues: “The United States and Russia both want the Assad regime in place to block the Sunnis. They both want the civil war to end, the Americans to reduce the pressure on themselves to aid the Sunnis, the Russians to reduce the chances of the Assad regime collapsing.”

Robert Fisk reported Sept. 30 that, “Six weeks ago, a two-civilian delegation from Aleppo, representing elements of the Free Syrian Army… met (secretly), so I am told, a senior official on the staff of President Assad. And they carried with them an extraordinary initiative – that there might be talks between the government and FSA officers who ‘believed in a Syrian solution’ to the war…. There was no demand – at least at this stage – for Assad’s departure.” There was a commitment “that all must work for a democratic Syria.” Fisk said Damascus agreed.

The Sunni jihadist/Islamist groups will have something to say about possible negotiations, which they have opposed in the past. No one knows how all this will turn out but it will come to a head sooner than later.