After 15 years, why aren't we asking about Iran's role in 9/11?

Fifteen years on from the 11 September 2001 terror attacks on the US, al-Qaeda is better-positioned than ever before. Its leadership held, and it has rebuilt a presence in Afghanistan. More importantly, al-Qaeda has built powerful regional branches in India, North Africa, Somalia, Yemen and Syria.

Rebranding itself away from the savagery of Iraq, al-Qaeda has sought to embed itself in local populations by gaining popular legitimacy to shield itself from retribution if, or when, it launches terrorist strikes in the West. This is proceeding apace, above all because of a failure to assist the mainstream opposition in Syria, sections of which were forced into interdependency with al-Qaeda to resist the strategy of massacre and expulsion conducted by the Assad regime.

The 9/11 massacre had not come from nowhere. In February 1998, Osama bin Laden, then-leader of al-Qaeda, plus Ayman al-Zawahiri and three others signed a document that said "kill the Americans and their allies – civilians and military – is an individual duty for every Muslim".

Al-Qaeda attempted to blow up US troops in Yemen in December 1992. Three months later, al-Qaeda attacked New York's World Trade Center, murdering six people. In November 1995, a car bomb in Riyadh targeted the American training mission for the Saudi National Guard, killing six people. In June 1996, Iran blew up the US military living quarters at Khobar Towers in Saudi Arabia, murdering 19 people.

Al-Qaeda played "some role, as yet unknown" in the attack, according to the 9/11 Commission. The US Embassies in Kenya and Tanzania were levelled in August 1998, slaughtering 224 people and wounding 5,000, mostly Africans. And in October 2000, a skiff containing two suicide bombers struck an American Naval vessel, the USS Cole, in the port of Aden, killing seventeen sailors.

The conspiracy theories about 9/11 are now a feature of life today. Often proponents will hide behind the façade of "asking questions". Instead of queries about jet fuel melting steel beams and nano-thermite, however, this inquisitiveness would be much better directed at the actual unanswered questions surrounding 9/11, which centre on the role of Iran.

In 1992, in Sudan, al-Qaeda and Iran came to an agreement to collaborate against the West "even if only training", the 9/11 Commission records. Al-Qaeda members went to the Bekaa valley to be trained by Hezbollah, Iran's Lebanese proxy. Hezbollah's military leader at that time, Imad Mughniyeh, personally met Bin Laden in Sudan to work out the details of this arrangement.

There is no doubt that training provided by Iran made the 1998 East African Embassy bombings possible, and after the bombing numerous al-Qaeda operatives fled unhindered through Iran to Afghanistan. The 9/11 Commission documented that over-half of the death pilots "travelled into or out of Iran" and many were tracked into Lebanon.

Iran and Hezbollah wished to conceal any past evidence of cooperation with Sunni terrorists associated with al-Qaeda

Senior Hezbollah operatives were certainly tracking some of the hijackers, in at least one case travelling on the same plane. The operational planner of 9/11, Khalid Sheikh Mohammad, lived in Iran for long stretches of the 1990s. To this day there is an extensive al-Qaeda network that feeds the global branches based in Iran, sheltered from US counter-terrorism efforts.

"Iran and Hezbollah wished to conceal any past evidence of cooperation with Sunni terrorists associated with al-Qaeda," the 9/11 Commission noted. But the connections were there, and "this topic requires further investigation". Sadly, such investigation has never occurred. Instead, the Islamic Republic has been brought into the fold, with billions of dollars released to it through the nuclear deal and a curious belief that Tehran can, or will, help stabilise the Middle East has taken hold.

Bin Laden had intended to drive the US out of the region with the 9/11 attack. "Hit them and they will run," he told his followers. This was a theme of his 1996 fatwa first declaring war on America. In this, he miscalculated.

The Taliban regime had sheltered Jihadi-Salafists from all over the Arab world. Some left over from the fight against the Soviet occupation; others on the run from the security services of their native lands or just wanting to live in a land of "pure Islam". Though the training and planning for global terrorism occurred in Afghanistan, most of al-Qaeda's resources were directed more locally, toward irregular wars, notably in Algeria, Bosnia, and Chechnya. Al-Qaeda trained up to 20,000 jihadist insurgents before 9/11. This sanctuary was lost in the aftermath of 9/11, something lamented by jihadi strategist Mustafa Setmariam Nasar (Abu Musab al-Suri).

Bin Laden had worked with Ahmad al-Khalayleh (Abu Musab al-Zarqawi), the Jordanian founder of what we now know as the Islamic State (Isis), to carve out a jihadi statelet in northern Iraq in the late 1990s led by a group called Ansar al-Islam.

After the Taliban's fall, al-Khalayleh moved into this area and into Baghdad in early 2002. After making preparations through Syria for the influx of foreign fighters, al-Khalayleh moved to the Ansar-held territory and waited for the US.led Coalition.

IS's predecessor planned - with al-Qaeda's blessing – to expel the Coalition forces and set up an Islamic state in Iraq that could then spread across the region, restoring the caliphate. But IS's methods brought it into frequent conflict with al-Qaeda, and by 2008 IS had been strategically defeated after provoking a backlash among Sunnis in Iraq. The distinctions between IS and al-Qaeda hardened thereafter until their formal split in February 2014.

IS, post-2008, changed some tactical aspects so as to bring the tribes back on-board but remained remarkably consistent in its approach, including the celebration of violence, premised on the idea of building an Islamic state as quickly as possible, which would force the population into collaboration with it and ultimately acceptance over time. In contrast, al-Qaeda placed ever-more emphasis on building popular support that would culminate in a caliphate when it had a critical mass.

The discrediting of IS's predecessor, operating under al-Qaeda's banner, damaged al-Qaeda so much that Bin Laden considered changing the organization's name. Events since then, above all allowing the Syria war to protract, allowed al-Qaeda to rebrand as "pragmatic", using IS as a foil, and recover.

Al-Qaeda, vanguard-style, took on the local concerns, worked to solve them, and in turn claimed the protection of the local population. Al-Qaeda has tangled itself so deeply into local dynamics, in Yemen and Syria most notably, that it would require a substantial local effort to root them out.

Unfortunately, the Western approach is making the problem worse. A good example came on Thursday night (8 September 2016) when the US launched air strikes against some leaders of al-Qaeda in Syria, now calling itself Jabhat Fatah al-Sham (JFS), which ostensibly disaffiliated from al-Qaeda in July in order to further this process of entanglement.

JFS claims it has no external ambitions and is working to break the siege of 300,000 people in the rebel-held areas of Aleppo city, yet it is attacked. Meanwhile, the US has done nothing about the thousands of Iranian-controlled Shia jihadists, tied into Iran's global terrorist network, who are the leading element in imposing the siege, and conducted these strikes likely in furtherance of a deal with Russia, which also helped impose the siege. JFS thus claimed that it is serving the Syrian people, while the US opposes the revolution and supports the pro-regime coalition.

"It is a highly unfortunate reality that many Syrians living in opposition areas of Syria perceive JFS as a more determined and effective protector of their lives and interests than the United States and its Western allies," wrote Charles Lister. The West has been unwilling to do anything to complicate the ability of the Bashar al-Assad regime to commit mass-murder for fear of antagonizing the Iranians and collapsing a "legacy-setting nuclear accord". While that remains the case, al-Qaeda will continue to gain power and acceptance as a necessary-evil in Syria, and the ramifications of Syria are generational and global.

It is true that there is far too much optimism in current assessments of IS's impending doom. The group will outlast the loss of its cities, and the misguided way the Coalition has conducted the war will provide conditions for a potential revival. Still, it is al-Qaeda that has the long-term advantage.

IS claimed sole legitimacy to rule, gained visibility and therefore followers. But as strategists like Setmariam understood, this made them visible to their enemies too, a toll that is beginning to tell, especially abroad. In Syria, formal al-Qaeda branches were never the organisation's only lever and al-Qaeda was much more interested in shaping the environment than ruling it. In essence, al-Qaeda will give up the name and the public credit for the sake of the thing – whether that's the popular understanding of the religion or the foundations of an Islamic emirate.

"IS wants the world to believe that it is everywhere, and ... al-Qaeda wants the world to believe that it is nowhere." That quip from Daveed Gartenstein-Ross neatly summarizes the trajectory of the two organisations. What can't be seen is harder to stop – al-Qaeda's counting on it.

Kyle W. Orton is associate fellow at the Henry Jackson Society and a Middle East analyst and commentator. Follow him on Twitter: @KyleWOrton