The rise of al Qaeda's affiliate in Syria, al-Nusra Front, which the United States designated a terrorist organisation last week, could usher in a long and deadly confrontation with the West, and perhaps Israel.
Inside Syria, the group is exploiting a widening sectarian rift to recruit Sunnis who saw themselves as disenfranchised by Assad's Alawite minority, an offshoot of Shi'ite Islam that dominates Syria's power and security structures.
Al-Nusra appears to have gained popularity in a country that has turned more religious as the uprising, mainly among Sunni Muslims, has been met with increasing force by authorities.
It has claimed responsibility for spectacular and deadly bombings in Damascus and Aleppo, and its fighters have joined other rebel brigades in attacks on Assad's forces.
According to Site Intelligence group, Nusra claimed responsibility in one day alone last month for 45 attacks in Damascus, Deraa, Hama and Homs provinces that reportedly killed dozens, including 60 in a single suicide bombing.
"In 18 communiqués issued on jihadist forums ... most of which contain pictures of the attacks, the al-Nusra Front claimed ambushes, assassinations, bombings and raids against Syrian security forces and 'shabbiha', pro-Bashar al-Assad thugs," Site said.
Members of the group interviewed by Reuters say al-Nusra aims to revive the Islamic Caliphate, which dates back to the Prophet Mohammad's seventh century companions, forerunners of the large empire that once stretched into Europe.
That prospect alarms many in Syria, from minority Christians, Alawites and Shi'ites to traditionally conservative but tolerant Sunni Muslims who are concerned that al-Nusra would try to impose Taliban-style rule.
Fear of religion-based repression has already prompted Kurds to barricade their quarter of Aleppo city and was behind fierce clashes between Kurdish and al-Nusra fighters in the border town of Ras al Ain in November.
The ideas of al-Nusra are also at odds with a new Syrian opposition coalition that was recognized last week by dozens of countries as an alternative to Assad and is committed to establishing a democratic alternative to Assad's rule.
Omar, a 25-year-old university graduate and former army conscript, said he deserted and joined al-Nusra in reaction to repression he experienced as a Sunni from Alawite officers who all but monopolize the army's higher echelons.
Prior to the revolt, Omar said he had sympathized quietly with Hizb ut-Tahrir, an Islamic international party with a vision for the restoration of the Islamic caliphate abolished by the secular Turkish strongman Mustafa Kemal Ataturk in 1924.
"Prayer in the army is banned, and if they suspected that you pray they would send you to the most remote posts," Omar said by phone from a rural area near Aleppo city.
"Our aim is to depose Assad, defend our people against the military crackdown and build the caliphate. Many in the Free Syrian Army have ideas like us and want an Islamic state.""We and other Islamists have gained a reputation as being able to hold our own in battle. Lots of people want to join Nusra, but we do not have enough weapons to supply all of them."