
Events in Syria over the last several weeks show signs of a looming regional sectarian conflict. This conflict is complicated and requires a deep understanding of many nuanced aspects. Therefore this analysis will be conducted in two parts: the first focusing on al-Qaeda’s operations and Iranian influence in Syria; the second
Al-Qaeda has been a prominent and growing player
There are places where their names are used interchangeably or both operate but do so separately; where they are distinct but cooperate on attacks; and where one or the other is the sole or prominent actor… Aleppo and Deir ez-Zor [are] cities where JN and ISI(S) function separately, Deraa as a city where JN maintains primacy, and al-Raqqa as a city where they are indistinguishable, although these dynamics are in constant flux.
Despite the confusing relationship, both groups have the same ideological goal of establishing a Salafist-jihadist caliphate, but their operational goals are markedly different.
JN is attempting to gain territory and establish a positive reputation among Syrians. With their public relations and social welfare programs, they are trying to project a moderate image of al-Qaeda. “By all
As noted above, JN is seeking to project the image of jihad that every Syrian Sunni can approve of. The goal of ISIS, however, is simply to spark a sectarian conflict that will lead to the establishment of a unified area of operation from Iraq to Lebanon. Their operations in Iraq have gained momentum in recent months, most notably with the recent spate of jail breaks

With ISIS sparking sectarian conflict on the Sunni side, Iran is fueling the fire from the Shia side. Iran is increasing its calls for Shia men to join the fight to protect holy shrines in Syria, principally the Sayyida Zaynab shrine in Damascus. The influx of independent Shia militias creates a command and control problem for the Syrian military. With the government not able to control all of these allied groups, the likelihood of ethnic cleansing against Sunni civilians increases
A struggle is underway between the two intellectual centers of Shia political power: Najaf, in Iraq, and Qom, in Iran… The former, which has strained itself to interpret events in Syria as a political struggle, and which maintains a certain theological distance from such matters, has urged Iraqi Shias to spurn the fight there and not fan the sectarian flames… In Qom, the situation is different. The Islamic Republic of Iran… has been issuing quite contrary edicts. Their version of Shi’ism merges the political and theological spheres and, through the counsels of the Supreme Leader Ayatollah Ali Khamenei, the faithful are enjoined to travel to Syria and fight against what they regard as a Sunni insurgency.
The Iranians are carefully crafting a narrative of a defensive jihad that is inspiring Iranian and Iraqi Shi’ites to fight the Sunnis all over Syria, ostensibly while defending the Sayyida Zaynab shrine. This is done through Iranian media campaigns within Iraq that take statements from Iraqi clerics such as Muqtada al-Sadr or Ayatollah Ali Sistani, and carefully highlight or omit points in order to paint a picture of the Iraqi clerics’ support for intervention in Syria. Additionally, these campaigns put out banners advocating Shia intervention with an approving picture of al-Sadr or Ali Sistani
With al-Qaeda and Iranian action increasing its tempo, the transition from nationalist civil war to regional sectarian conflict will occur more rapidly. With little being done to stem those actions by outside forces the situation will get worse, including a growing number of ethnic cleansing incidents. US policymakers should implement plans that reduce both al-Qaeda and Iran’s capabilities in the region. In Syria, plans should include increased sanctions that specifically target oil exports that are financing al-Qaeda. In Iraq, monetary aid should be given to bolster the Iraqi government’s ability to counter ISIS operations and should include funds ear-marked for programs countering Iranian clerical influence in Iraq.