In a chilling alliance that could turn conventional wisdom about the current Syria debate — and the revolution’s players — on its head, signs continue to mount that show al-Qaeda is working not against Bashar al-Assad but in concert with the dictator.

This includes assassinating key Assad opponents, coordinating attacks, not targeting each other’s positions and helping push a War on Terror narrative to keep Assad in power.

It would hardly be unprecedented given the alliances between al-Qaeda and Assad’s Shiite friends, Iran and Hezbollah, as well as Assad’s favor shown to Sunni terrorists Hamas and Islamic Jihad. It could also be a devastating win-win for the terror organization that has been written off as crippled by President Obama while busily retooling its strategy to flourish in the new global environment.

After Ayman al-Zawahiri took the helm in 2011, he laid out a blueprint for al-Qaeda’s next chapter: taking advantage of Arab Spring crises, fomenting chaos behind the scenes, and souping up the public relations effort — not just recruiting “lone wolves” with the glossy Inspire magazine but playing upon the media and public sentiment to stealthily work to their advantage.

This guidance began even before the death of Osama bin Laden, as shown in a 2005 letter from Zawahiri to al-Qaeda in Iraq leader Abu Musab al-Zarqawi intercepted during a counterterrorism operation. In the letter, Zawahiri said the Islamic world is “like a bird whose wings are Egypt and Syria, and whose heart is Palestine.”

The Egyptian doctor chided Zarqawi for not thinking more before attacking Shiites after the fall of Saddam Hussein. “And even if we attack the Shia out of necessity, then why do you announce this matter and make it public, which compels the Iranians to take counter measures? And do the brothers forget that both we and the Iranians need to refrain from harming each other at this time in which the Americans are targeting us?”

“One of the most important factors of success is that you don’t let your eyes lose sight of the target, and that it should stand before you always,” Zawahiri added. “…Courage in a man does suffice but not like the courage of one who is wise.”

The Iranians aren’t taking countermeasures against al-Qaeda forces supposedly threatening their brother Assad, yet continue to offer haven to the terror group’s leaders. But then again, Assad isn’t taking countermeasures against the al-Qaeda strongholds, either.

It’s just one omen that has alarmed Syrians about an unholy alliance being overlooked by the West.

Zawahiri has played into the deception with well-timed statements calling for Assad to be overthrown, reviving Syrians’ memories about how Assad gave Zarqawi’s fighters a transit route and safe haven.

“The Syrian regime helped al-Qaeda kill Americans in Iraq,” Maroneh native, Christian and Boston diaspora leader Essam Francis told PJM in March 2012. “For al-Zawahiri to say something against the Syrian regime is not right. He did a favor for the regime to do that. He gave them reason to kill a lot more people.”

The Zarqawi name still keeps popping up in this conflict, as well: the late al-Qaeda in Iraq leader’s brother-in-law was reportedly killed in Syria this January. Two Zarqawi cousins popped into Syria last October but returned to Jordan “because there was no fighting against Syrian regime troops” and were detained by Jordanian authorities.

The State Department designated the al-Nusra Front as an alias for al-Qaeda in Iraq in its December terrorist designation. The Islamic State of Iraq and Syria (ISIS) also sprang from al-Qaeda in Iraq and attracts most of the foreign fighters within Syria.

“America, its agents and allies want you to shed your blood and the blood of your children and women to bring down the criminal Baathist regime, and then set up a government loyal to them and to safeguard Israel’s security,” Zawahiri said in June, also claiming that through support for Assad the conflict “revealed the ugly face of Iran.”

The same Iran that has been sheltering al-Qaeda members and serving as a critical transit point for al-Qaeda funds under an agreement with the government in Tehran.

“Iran is the leading state sponsor of terrorism in the world today. By exposing Iran’s secret deal with al-Qa’ida allowing it to funnel funds and operatives through its territory, we are illuminating yet another aspect of Iran’s unmatched support for terrorism,” said Under Secretary for Terrorism and Financial Intelligence David S. Cohen in placing sanctions on the six al-Qaeda leaders of the Iranian base.

The leader of that operating agreement, senior al-Qaeda facilitator Ezedin Abdel Aziz Khalil, is Syrian. The U.S. is offering a $10 million reward for Khalil, who has lived comfortably in Iran since the 2005 deal was forged.

After the Iraq war, Assad was under pressure from the U.S. to provide intelligence on al-Qaeda and, at the very least, not give the impression that his country was safe passage and haven for al-Qaeda in Iraq. So the regime jailed a bunch of guys it labeled al-Qaeda, though one political prisoner during that time saw a far different story.

Ahed Al Hendi, a student dissident who fled Syria five years ago after imprisonment and torture by Assad’s regime, told PJM his cell was next to Mohamed Dakhnous, a prisoner tagged as al-Qaeda. Dakhnous asked Al Hendi if he prayed, and began reading the Quran aloud. The guard threatened torture if Dakhnous kept reading out loud, so Al Hendi finally told the al-Qaeda suspect that he was Christian.

“You follow Jesus?” Dakhnous asked.

“Yes,” Al Hendi replied.

“Then we are the same!” Dakhnous exclaimed.

He was no member of al-Qaeda but an unemployed guy in his 20s who was approached by an Assad-linked Palestinian group called the General Command to go fight in Iraq. Dakhnous found a job and ended up not going to war, but was arrested by the Assad regime two years later and charged with being al-Qaeda. “This was done purely for show in order to convince the U.S. that they were serious about arresting terrorists,” Al Hendi said. Meanwhile, the Syrian government never arrested al-Qaeda recruiters such as Abu Al Qaqa, a radical Sunni cleric reportedly on the dole of the regime.

As its power has grown, al-Qaeda has been handily taking out longtime foes of Assad and advocates for a democratic Syria.

Father Paolo Dall’Oglio, an Italian Jesuit priest who called Syria home since the late 1970s, welcomed tens of thousands of Syrians, the majority of those Muslim, through his Monastery of Saint Moses north of Damascus each year. As Assad’s regime waged a bloody crackdown on peaceful Arab Spring demonstrators beginning in 2011, Father Paolo became an icon of the revolution, a constant leader of opposition protests and a thorn in Assad’s side until the regime finally expelled him from the country in June 2012. Syria’s state news agency smeared the priest a year ago, saying he was on al-Qaeda’s payroll.

By January, Father Paolo was back. He wanted to bring all factions of the opposition together for cohesive dialogue with the goal of moving forward as one and ousting Assad. He was kidnapped at the end of July by al-Qaeda fighters of the ISIS and killed, thereby ridding Assad of a unifying figurehead against his regime.