WASHINGTON — Since the onset of the war in Syria, the Obama administration has openly lent its support to the Free Syrian Army along with many Western nations, including France, Turkey and the Gulf Arab states — particularly Saudi Arabia and Qatar — in an open and active attempt to bring regime change to Syria by toppling the country’s secular President Bashar Assad through the Friends of Syria pact.

Though Assad took 88.7 percent of the vote in the recent presidential elections, U.S. Secretary of State John Kerry continues to say that Assad’s days are numbered. An increasing number of reports have emerged that the United States is continuing to aid and train rebels who are active in Syria’s war in neighboring country Qatar — a Gulf state that supplies weapons and aid to the Islamic State of Iraq, a branch of al-Qaida that operates inside Syria fighting the Free Syrian Army and competes with another al-Qaida offshoot, the Saudi-backed Jabhat al-Nusra, or the Nusra Front.

What makes arming the rebels more complicated, though, is footage that has surfaced of members of the Free Syrian Army merging with terrorist organizations such as the Nusra Front and the ISIS operating there, where U.S. military weapons — which the U.S. had originally provided to the Free Syrian Army — are falling into the hands of the same terrorist groups the U.S. government is fighting in its so-called “war on terror” in other regions of the Middle East.

A deeper dive into the Syrian conflict reveals far more than a simple uprising by the Free Syrian Army, however. On closer inspection, it’s a proxy war with religious tendencies that has turned Syria’s original revolt against Assad into a deadly sectarian civil war that has taken the lives of over 160,000 people and created one of the largest refugee crises in history.

Given the presence of military and non-lethal aid sent to the opposition by the international community, MintPress News sought to provide an overview of the rebel groups operating in Syria and break down their composition, goals and aims to determine just where that American and Western aid is going and what it might be used for.

Free Syrian Army, hijacked

In November 2013, soldiers with the Free Syrian Army were guarding stockpiles of U.S.-supplied weapons in Atmeh when other opposition forces approached. There had already been fissures between different rebel groups — split particularly by religious ideology — but the Free Syrian Army was not prepared for what happened next. Members of the Islamic Front militia surrounded the guards and seized the Free Syrian Army’s northern headquarters, warehouse and arms.

Little is known for certain about how exactly the incident went down, but what is known is that the moderate Free Syrian Army lost weapons — including many likely provided by the U.S. — to a militant Islamic group

“They were caught by surprise, I think, because of the de facto ceasefire agreement between the groups,” Hart Uhl, program director at Syrian Center for Political and Strategic Studies, told MintPress. But, “as soon as that happened, they thought ‘we need to address this situation.’”

The event highlighted for the international community the differences between the Syrian rebel groups, which often found themselves at odds with each other since the civil war broke out.

Immediately after finding out about the raid, the U.S. announced a suspension of “non-lethal” aid to Syrian opposition forces, seeming concerned about whose hands that aid may actually find itself in. Of particular concern were Salafist extremists — many of whom are connected to the al-Qaida branches of the Nusra Front and the ISIS. For Western powers inclined to aid rebel forces to encourage regime change in Syria, it was a stark reminder of just how fluid — if not completely volatile — the opposition is.

Free Syrian Army

When many Western leaders speak of the “Syrian opposition” on the ground, they are likely referring to the Free Syrian Army, which is ostensibly a group of disaffected military personnel who defected after refusing to follow President Assad’s orders to shoot on Syrian civilians. Trained and heavily armed, the former army officers rallied around Riad al-Asaad, a colonel in the Syrian Army.

“These were guys who were in charge of weapons,” Uhl noted. “As soon as the civil war started, they knew they couldn’t be involved in the army anymore.”

They took their weapons and training and joined demonstrators in opposing the regime.

In a March 2013 article titled “The Free Syrian Army Doesn’t Exist,” however, Aron Lund, editor of the Carnegie Endowment for Peace’s Syria in Crisis Blog, argued that the Free Syrian Army was likely the creation of Turkish intelligence operators. Asaad announced the formation of the group while in Turkey in July 2011, he has spent more time in the neighboring country than in Syria itself, and he was reportedly there when the Free Syrian Army warehouse was overrun in November 2013.

The Free Syrian Army has also been seen as the military wing of the Syrian National Council, an exiled political group based in Istanbul.

“The FSA has become a one-stop for everything about the opposition,” said Sharmine Narwani, a writer on Middle East geopolitics and former Huffington Post Mid-East blogger who last visited Syria on a reporting trip in March and April.

“There’s what’s known as the unconventional warfare doctrine: You create a brand by creating an exile government, then creating an army. The FSA suited that purpose.”

Uhl suggests a number of Free Syrian Army leaders are local, “from civilian ranks who gained experience on the ground along with a large following.”

However, Narwani argues that although these local factions pledged allegiance to the Free Syrian Army, they have little contact with its leadership and operate independently, limiting the opposition structure’s role.

“There never was a chain of command,” she told MintPress News. “The leadership was always outside Syria, so other groups on the ground were owning the battle.”

Islamic extremist groups

Three Islamic extremist groups appear to play major roles in the opposition:the Islamic Front, the Nusra Front and the ISIS.

A coalition of al-Qaida-linked groups, the Islamic Front was reportedly responsible for the November raid on the Free Syrian Army stockpiles. However, following inner-coalition rivalry and conflict with the ISIS, the group’s power is believed by many to be on the wane, leaving a vacuum to be filled by the Nusra Front and the ISIS.

While the Nusra Front maintains its association with the global al-Qaida network, the ISIS severed its ties with the terrorist organization after al-Qaida leader Ayman al-Zawahiri repudiated the ISIS for engaging in hostilities with the Nusra Front.

Despite their differing relationships with al-Qaida, both organizations share a primary goal of creating a Salafist state in Syria under Taliban-style rules. However, both appear to be treated differently by Syrians themselves.

The ISIS, heavily comprised of foreigners, is seen as an intruding influence, while the Nusra Front has maintained stronger local lies since it merged with the Syrian Muslim Brotherhood early in the conflict.

According to Uhl, the Nusra Front was actually created by the ISIS when members of the group wanted to get involved in the Syrian conflict but didn’t want to lose their own fighters in West Iraq.

“They created something of a Syrian arm of themselves,” Uhl said. “Al-Nusra started not following the ISIS’s orders and that started creating schisms.”

Uhl adds that after Assad abandoned control in parts of the country taken over by the opposition, Nusra Front members — who were also part of local communities — started creating their own government and set up Salafist Shariah commissions and courts. The ISIS, however, is seen as being more forceful in their implementation of Salafist Shariah, Islamic law not followed by the majority of the Muslims around the world.

“Al-Nusra is perceived as being predominantly Syrian and not as heavy-handed in the way they push their ideals in the areas they control,” he said.

Narwani agrees with this assertion.

“I know people who will regularly talk to al-Nusra because they’re Syrian, but they will not to talk to foreign extremists who have no connections to the community or vested investment in the people,” she said.

Given their continued ties to al-Qaida, their tactics and the objective of a Salafist Shariah-based state, the U.S. State Department — along with several other foreign governments — labels the Nusra Front a “terrorist organization.”

Uhl suggests that such a label “contributes to their legitimacy” in the conflict, but also contained within is an effort to get “al-Nusra to go from the dark side to the light side.”

“That’s just not going to happen,” he said. “They are just not going to turn away from their ideology.”

The distraction of a religious proxy war

Many observers point out that even more consequential is the effective proxy war taking place in Syria. This proxy war involves Saudi, Qatari and Turkish factions vs. Irani, Lebanese Hezbollah and Syrian religious minorities, and it revolves around the age-old conflict between adherents within the Sunni and Shiite Muslim orders.

“Until recently, observers have tried to steer clear of the notion that a Sunni-Shia conflict — a geopolitical battle between members of different Muslim sects — is engulfing the Middle East,” wrote Nathan Gonzalez, author of “The Sunni-Shia Conflict: Understanding Sectarian Violence in the Middle East,” in The Diplomat.

“However, with the latest violence in Syria, this dynamic has become all but impossible to ignore. This conflict is largely fueled by the battles between Shiite Iran and its Sunni neighbors,” he continued.

“Iran is already deeply invested in not losing its only ally in the MIddle East,” Gonzalez told MintPress News, explaining Iran’s support for the Shiite-dominated government of Assad. Meanwhile, Saudi Arabia, Qatar and Turkey have all fallen on the side of the opposition, at least partly for the opposing reason of toppling Assad in favor of a Sunni-Salafist-leaning regime.

While the conflict started as a small protest, Gonzalez explains that it developed into something much larger that brought regional players into it, “which was bound to happen because of Syria’s borders which puts it in the middle of the regional politics.”

“When you have an Alawite [Shiite] regime aligned with Iran ruling a country in which the majority of the opposition is Sunni, it’s an invitation to major actors to get involved on the basis of this sectarian conflict in the Middle East,” he said.

However, according to Ali Al-Ahmad, director of the Washington-based Gulf Institute and a scholar on Saudi politics, Assad’s own Syrian Army consists of Sunni soldiers who believe the sectarianism that is playing out in the conflict today was non-existent until the Nusra Front and the ISIS came into the picture. Sectarianism only came into play, he says, after the destabilizing influences hijacked the Free Syrian Army revolt.

This is not to say that religion is the sole factor partitioning sides, whether it be Sunni vs. Shiite or religious vs. secular, says Ahmad.

“It’s partly about the struggle between Sunni and Shiite,” he explained.

“Not all Assad [supporters] are Shiite and not all of the opposition are Sunni. It’s more complex than that. Assad would never have survived if it wasn’t for the Sunni members of his army.”

Equally important to Ahmad are the individual geopolitical factors of interest to Saudi Arabia, Qatar and Turkey, who are all competing for influence in Syria to further their political gains.

For Saudi Arabia, the concern is the potential threat to the Saudi monarchy posed by nations like Syria and Iran. Nations like these bring attention to the silenced revolution taking place in Saudi Arabia’s oil-rich provinces among Shiite minorities who have been uprising against the Saudi monarchy and many Sunni Saudis who demand that they not be treated as second-class citizens.

“A strong country — whether Sunni or Shiite — might be a problem to the Saudis,” Ahmad told MintPress. “Most recently, if you look at Egypt, there’s a trend of collapsing monarchies [dictators] and the success of Qatar has embarrassed them. Their people look at the cars and wealth and wonder why they can’t have that, too.”

Qatar and Turkey supported the Muslim Brotherhood in Egypt and even helped former Egyptian President Mohammed Morsi get elected, but they accuse Saudi Arabia of orchestrating a coup to oust Morsi from power and to keep current President Abdel-Fattah el-Sissi in power because he complies with Saudi influence there and has even raked in billions of dollars in aid from Saudi Arabia already.

For Turkey, the goal is simply to gain more regional influence: first through supporting the Muslim Brotherhood in Egypt, then in Syria, despite Syria’s Muslim Brotherhood merging with the Nusra Front.

“Having in their mind what was a muslim Brotherhood regime in Syria would have given them [Turkey] an advantage,” he said.

U.S. aid and arms falling into al-Qaida’s hands

In his address to West Point on May 28, U.S. President Barack Obama promised more aid to rebel groups.

“I will work with Congress to ramp up support for those in the Syrian opposition who offer the best alternative to terrorists and brutal dictators,” he told graduating cadets, adding that he would also aid neighboring countries Jordan, Lebanon, Turkey and Iraq “as they contend with refugees and confront terrorists working across Syria’s borders.”

This was music to Hart Uhl’s ears.

“There have been many, many missed opportunities along the way where we could have played a real role in ending the conflict,” the program director of the Syrian Center for Political and Strategic Studies said. “The U.S. could have played a much more major leadership role.”

When asked if he has any concerns about a repeat of the November raid that might put U.S.-supplied weapons in extremist hands, he dismissed the risk.

“I don’t think any of the weapons taken from that warehouse were American,” Uhl said. “The weapons that are going to the armed opposition are only being given to a select groups who are highly vetted and they have been given in very limited numbers to very specific people.”

Narwani is not so certain.

“There’s no clear understanding of where that support would go,” she said. “The State Department can’t even name the moderate opposition. There is also the problem of the fungibility of the weapons between these groups as members move from one group to another to go wherever there’s funding.”

“We saw al-Nusra with [an American-made] Tow missile,” she added.

Gonzalez believes that the Obama administration’s reluctance to become more involved relates to Iran, as the U.S. doesn’t want to isolate the Shiite nation even more during talks over Iran’s nuclear program.

“You have a balancing act,” he explained. “On the one hand, Syria is Iran’s only true ally, so you would think we would want to get rid of Assad very quickly and Iran would be defeated.”

However, Obama would not want to endanger the legacy of achieving a nuclear deal so “we don’t want Iran to feel completely backed into a corner.”

“If we commit airstrikes or other military engagement in Syria, we are going to have to get involved militarily in Iran,” Gonzalez, the author, said.

And this is a conflict most Americans don’t want.