The war in Syria seems to be one disaster after the next. Last week, credible reports emerged that upwards of a thousand people died on the outskirts of Damascus after the Assad regime used chemical weapons against them. After trying to delay United Nations weapons inspectors, the Assad regime now faces an international response, possibly in the form of a military strike.

But the biggest disaster to befall the country may not be the alleged use of chemical weapons by Syrian President Bashar al Assad, an incident now being investigated by a team of United Nations inspectors. Rather, it‘s the continued fracturing of Syrian fighters – a development that threatens any hope for reconstruction once the fighting dies down – that is sparking such concern and caution about the two-year civil war.

In a video statement released on Aug. 22, the five front-line commanders from the opposition-backed Supreme Military Council announced they were abandoning the group and choosing instead to work with any group willing to fight Assad. They tendered their resignation while sitting in front of the black flag of Jabhat al Nusra, a key opposition group with growing ties to al Qaeda in Iraq – implying they have rejected U.S. demands not to work with jihadists.

The council, formed in December 2012, was meant to consolidate the various rebel factions into a unified command structure. It never really worked – the SMC had little legitimacy, and the chains of command to each front were only as good as the individual commanders leading them. Though it had the potential to serve as a check on the radicalization of the opposition movement, that potential now seems further away than ever before.

“It’s really sad to see,” Elizabeth O’Bagy, a senior research analyst at the Institute for the Study of War who just returned from a research trip to Syria, told Defense One. “Islamic movements are taking over the council and people feel they can’t fight back.”

The Syrian resistance has become increasingly radicalized over the last two years. “Especially in Aleppo, but also in the rebel-controlled North, you see the Islamic State of Iraq taking over local councils entirely,” she says, referring to the official name for al Qaeda’s branch in Iraq.

The SMC is nominally led by Salim Idriss, who chairs its Joint Staff. “It never really exercised its power,” said Kirk Sowell, CEO of Uticensis Risk Services and an Arabic language researcher. “They failed to remove troublesome commanders from Aleppo and Dira, but they could have become a kind of Defense Ministry.”

Yet this recent defection of its top leaders, Sowell says, shows that not only does Idriss lack authority over his own commanders, but that the SMC “is a total non-entity” inside Syria.

Two major setbacks seem to have broken the SMC: the collapse of last month’s Latakia Offensive and last week’s apparent use of chemical weapons in the suburbs of Damascus. The offensive, led and endorsed by Idriss, failed to dislodge regime forces from Syria’s northwest coast. Days later, the Assad regime responded by reportedly unleashing chemical weapons against upwards of a thousand civilians. Both were were devastating blows to the opposition.

“This is incredibly dangerous in terms of the radicalization of the population,” O’Bagy says. “If the international community does not respond to chemical weapons use, the radicalization of the population might be irreversible.”

In the video, SMC spokesman Fatih Hassun, the commander of the Homs Front, repeatedly uses the phrase “majusi” to describe the enemy. “It is the most sectarian way of framing the conflict,” Sowell said, as it turns the war into a Sunni-vs-Shia battle.

While the UN continues to inspect the chemical attack, while dodging sniper fire, yet another worrying development is taking hold among the regime forces. “The regime is evolving into a variety of militia-like forces,” O’Bagy said. “I was amazed when I was in Aleppo that the regime largely withdrew from the city and relied instead on local militia groups.”

These militias consist of both local fighters and foreign fighters, mostly from Hezbollah and Iran. “I am amazed at how many pro-regime militias have Farsi-speaking advisers with them,” she said. “Iran is heavily influencing the regime’s decision-making process.”

Complicating matters is the growing presence of Iranian fighters at Assad’s chemical weapons facilities. In a February 2009 report, Janes Defense Weekly detailed an agreement between Damascus and Tehran to upgrade Syria’s chemical weapons. It’s unclear whether Iran had any say in the most recent chemical attack, but there are growing reports that Iranian fighters are guarding Syria’s chemical weapons facilities.

As the world ponders what comes next for Syria, the involvement of Iran and Hezbollah weighs heavily. And the prospect of more direct involvement by Tehran has many analysts worried. Moreover, the increasing radicalization by Syrian rebel groups, including the SMC’s decision to work directly with the local al Qaeda branch, bodes poorly for any future scenario.

“It’s in the U.S.’s interests to try to end things as quickly as possible,” O’Bagy said. “There are a lot of moderates still fighting, and supporting them is critical.”

Unfortunately, it is the jihadist militia groups that have focused so much on controlling territory and governance, while the moderate groups have done most of the fighting, weakening any hope of fostering and rebuilding a civil society after the war ends.

After the ambiguous results at the battles for Latakia and Aleppo, it seems clear that neither side is eking out a decisive advantage to win. Assad’s growing use of militias to fight instead of his own military suggests that not only is he losing control, but that local groups will be able to continue fighting if he’s swept from power. And the jihadization of Syria’s resistance movement also suggests that the war-after-this will be even more brutal as time moves on.

Yet the biggest question of all -- can a U.S.-led military strike improve the situation inside the country? -- remains unanswered.