Game-Changer: Signs of the al-Qaeda-Assad Alliance

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.

Last week, the ISIS kidnapped and executed activist Dr. Mohammed al-Abyad in Aleppo. Two days earlier, the ISIS killed an opposition poet, Mohammed Hamadeh. Last month a Free Syrian Army commander, Kamal Hamami, was shot in cold blood at a checkpoint by the ISIS. When a high-profile opponent of Assad's is rubbed out, there's a consistent calling card: al-Qaeda.

Assad appears OK with losing a building now and then by a car bomb -- bombings that never hit too close to his home and that come with ample warning anyway. Al-Qaeda units, meanwhile, get left alone by Assad's forces. "They never touch them," Al Hendi said.

And in a grotesque PR stunt, they've even coordinated on attacks.

Former Syrian Ambassador to Iraq Nawaf Fares, a 35-year regime operative who defected in July 2012 after the killings grew to be too much, told the Telegraph of the blurred lines between regime and jihadists in attacks such as the May 2012 suicide bombings outside a military intelligence building in the Damascus suburb of al-Qazzaz.

"I know for certain that not a single serving intelligence official was harmed during that explosion, as the whole office had been evacuated 15 minutes beforehand," Fares said. "All the victims were passers by instead. All these major explosions have been have been perpetrated by al-Qaeda through cooperation with the security forces."

Backing up cooperation claims from other defectors and activists, Fares said the relationship goes back to 2003 and the U.S. invasion of Iraq. "The regime in Syria began to feel danger, and began planning to disrupt the US forces inside Iraq, so it formed an alliance with al-Qaeda," he said. Also a onetime top security official, he said the Syrian regime still has "liaison officers" tasked to work with al-Qaeda.

In the prescient interview, Fares added: "Al-Qaeda would not carry out activities without knowledge of the regime. The Syrian government would like to use al-Qaeda as a bargaining chip with the West – to say: 'it is either them or us.'"

Another defector, top Air Force intelligence aide Affaq Ahmad, confirmed that the jihadists don't get into conflicts with the regime forces. "They also decline to get into fights in the coastal areas due to an agreement between them and the regime that had been brokered by the financial backers of these brigades," Ahmad said in an interview after fleeing Syria. "Actually, the jihadist groups and brigades were very useful for the regime because they provided a justification for the regime's insistence on a military solution, and provided some legitimacy under the cover of the War on Terror."

Under that agreement, he added, the regime accepted the killings of minorities including Assad's own Alawite sect "in order to use that to convince these minorities to rally around the regime and hold on to it."

Assad has never been particularly religious and the Alawites have not been exclusively behind Assad. "He's always used them," Al Hendi said. "I don't think he's sectarian in a spiritual way; he's using Alawites only now to protect himself."

Al-Nusra has already admitted to being in a deal with the Assad regime -- holding fast to the Deir Ezzor oil fields and reaping sweet payouts in return.

Abdulrahman Alhaj, a professor and member of the General Secretariat of the Syrian National Coalition, told PJM that Assad "has too much information about [al-Qaeda] in many ways."

And Assad feels that if he is taken out or taken to the brink, Alhaj added, the ultimate revenge is sharing his WMDs with the terror organization -- something he may do anyway in backroom deals.

"He'll try to make it easy for them because he wants to -- he will try to punish the international community," said Alhaj. "How he can do that -- he can give them his chemical weapons."

"It's a very dangerous scenario," he added.

When PBS' Charlie Rose asked Assad in a sit-down interview Sunday about what kind of retaliation could be expected if the U.S. launched airstrikes against the regime, he cryptically responded, "You should expect everything."

"You should expect everything, not necessarily through the government. It's not only -- the governments are not only -- not the only player in this region," Assad added. "…Expect every action. Everything."

A handful of Senate aides contacted by PJM said they didn't know if the alliance of al-Qaeda and Assad was being discussed with lawmakers in closed-door Syria briefings.

Assad needs the situation on the ground to look chaotic enough to keep from being ousted. Al-Qaeda enjoys a safe haven and access to stockpiles of weapons of mass destruction. And if Assad should fall, al-Qaeda can take advantage of the vacuum, though it does run the risk of having to deal with a president who's not compliant like Assad.

"Assad today is trying to convince the West that he is secular and liberal and that he is fighting Islamic extremism. Those who work in the field of politics, however, know Assad’s regime very well. They know it is nothing more than an extension of the extremist political and religious Iranian regime," Al Arabiya General Manager Abdulrahman al-Rashed wrote in March.

"His father adopted the case of Arab Baath to justify his seizure of power and continuity of sectarian rule. After him, his son sought the company of long-bearded men from supreme leader Khamenei to Hassan Nasrallah. He resorted to holding Islamic jihadi conferences in Damascus," al-Rashed continued. "After the revolution erupted, he now speaks of secularism and claims it!"

Images of jihadist atrocities have also shown timing to play into a PR strategy, including the grisly execution video from spring 2012 released to the New York Times just as Congress was debating Syria.

In another aptly timed move, al-Qaeda declared war today on the Free Syrian Army -- in particular, the secular brigades most likely to be vetted and cleared -- just in time to attempt to seize CIA arms deliveries beginning to flow to the rebels.

"The Assad regime...will increase extremism in Syria," said Alhaj. "That will affect all the people of the world."