This month marks five years since the start of the Syrian uprising—a movement that, for a brief period in March 2011, looked like it might bring peaceful change to an authoritarian state. By that point, the presidents of Tunisia and Egypt had already stepped down amid protests, seemingly marking a nonviolent end to decades of dictatorial rule in each country. Back then, it was puzzling to hear Syrian President Bashar al-Assad insist in justifying his crackdown on the opposition—a crackdown that had already killed more than a thousand civilians by the end of the summer—that the protesters who wanted democratic reform were “terrorist groups.”

But something had happened in the interim that helped change the character of the uprising, and played a role in turning the country into the battlefield it is today, in which major combatants—most notoriously ISIS and its local rival, the al-Qaeda affiliate Jabhat al-Nusra—are indeed terrorist groups. And as Charles Lister, a resident fellow at the Middle East Institute, recounts in his new book The Syrian Jihad, Assad fulfilled his own prophecy about the terrorist menace in Syria. On March 26, Lister writes, “a presidential amnesty was issued for the release of approximately 260 prisoners from Sednayya,” a prison outside Damascus. “Although claims continue to differ over the precise breakdown,” he continues, “it appears clear that the large majority of those were Islamists of one kind or another. … This may have been an attempt to appease the growing anti-government sentiment across the country; but it is more likely that it was yet another devious attempt by the Assad regime to manipulate its adversary, this time by unleashing those it could safely label as ‘jihadist’ or ‘extremist’ among its ranks.” Assad granted another major amnesty for prisoners that June.

Those moves weren’t enough, by themselves, to turn what had largely been a secular opposition movement into a jihadist juggernaut, but as Lister told me recently, the prison releases helped activate a terrorist infrastructure that was already latent in Syria. By the time the insurgent group known as the Islamic State of Iraq sent emissaries to set up a Syrian branch in August 2011, much of the work was already done. One result was ISIS—the Islamic State of Iraq and Syria—which Abu Bakr al-Baghdadi declared in 2013, announcing the merger of the Islamic State of Iraq with its Syrian affiliate. (The leader of the Syrian branch, Abu Mohammad al-Jolani, rejected the merger; while some of the group’s fighters joined the new ISIS, Jolani’s group Jabhat al-Nusra remained independent from, and became a rival to, Baghdadi’s.)

Five years after the emergence of peaceful protests against Assad’s rule, Syria is witnessing the first sustained reduction of violence since the eruption of the country’s civil war. A “cessation of hostilities” backed by Russia and the United States is entering its third week. (The deal does not apply to either ISIS or Jabhat al-Nusra.) Diplomats are once again meeting in Geneva in search of an agreement that might stop the bloodshed, and are cautiously welcoming a surprise gesture by Russia to withdraw the “main part” of its forces from Syria after more than five months of bombing to shore up the Assad regime. I spoke with Lister recently about the evolution of Syria’s uprising, from its hopeful beginnings to its destructive present. An edited and condensed transcript of our conversation follows.

Kathy Gilsinan: A lot of people place the start of the Syrian uprising on March 15 during the protests in Aleppo and Damascus five years ago. But I’m interested in a later point you describe in your book, which is March 26, when Assad, in what seemed like a concession to protesters, granted amnesty to 260 people in Sednayya prison. Who were they and why were they important to what’s followed?

Charles Lister: Up until this point, the protest movement was non-religious; it was inherently populist and nationalist in its orientation. I wouldn’t necessarily go as far as to say that those first 260 people released fundamentally transformed the uprising at that point, but [their] release opened the gates for the emergence of an Islamist component within the uprising—specifically, eventually, a militant Islamist component. And of course that took a while to significantly take root, but it was those initial releases that allowed the quite dramatic emergence, and then growth, and then consolidation of Islamist and jihadist militancy, to acquire the kind of prominence that it has had for the last couple of years or so.

Gilsinan: So how long did that take, and what was the process of consolidation like, roughly speaking?

Lister: Taking into account the first amnesty in March, and then the second big one in June—both of those combined placed dozens and dozens of convicted or accused al-Qaeda-affiliated jihadists out into various areas of Syria. As soon as they were released, they basically went to pre-existing al-Qaeda safe houses in places like Homs and Aleppo [and] outside Damascus. That jihadist infrastructure was already there before the uprising began, but it was that network that was activated by Abu Mohammad al-Jolani, who would go on to create Jabhat al-Nusra.

The decision that was made in Iraq in the summer of 2011 to try and establish a Syrian wing of [what was then the] Islamic State in Iraq was very easy to activate, precisely because that network already existed across Syria. From Jolani’s arrival [from Iraq, where he was the Islamic State of Iraq’s chief in Ninevah province] in August, it took roughly four to six weeks for Jabhat al-Nusra to be established as an organization with a presence in multiple provinces.

Gilsinan: Your book says that Syria’s “flirtation” with jihadism had begun long before [the uprisings of 2011], right after Bashar al-Assad took power from his father in the early 2000s. What did this flirtation entail, and how did these networks get set up?

Lister: It was basically the result of a strategic decision within Bashar al-Assad’s intelligence apparatus to try and infiltrate, in order to manipulate, Sunni jihadist militants to basically act on behalf of Syria’s foreign-policy interests. Actually some of this dates back just to before Bashar al-Assad’s term in power, to the late 1990s, but certainly there was a realization that Sunni jihadist militancy was going to take root in some areas of the country, and whether or not it was going to be combatted, and whether or not it would become a useful tool of foreign policy was the argument that took place in decision-making circles. Ultimately, jihadists were exploited and manipulated in order to serve Syria’s foreign-policy interests.

“Jihadists were exploited and manipulated in order to serve Syria’s foreign-policy interests.”

The best example of that came with the U.S. invasion of Iraq, [which was] obviously seen as against Syria’s interests in the region. Very quickly, within the first 10 to 11 days of the invasion, as many as 11,000 Syrian jihadis, and a few Lebanese, were bussed in Syrian government buses through open border crossings into [Iraq]. A flow of jihadist militants actually came back from Iraq into Syria [around 2007] because they were feeling pressure from the very beginning of the U.S. surge and tribal uprisings in places like Anbar province. That backflow into Syria obviously created a new threat, so many of those fighters were re-exported to Lebanon.

This came [during] a period of time where the Syrian Army had just withdrawn from Lebanon. So in a sense the re-exporting of these jihadists into Lebanon was an attempt to continue, albeit covertly, Syria’s attempts to undermine certain political factions within the Lebanese dynamic.

When these militants went into Lebanon, Syria’s military intelligence specifically exploited relationships with a group—Fatah al-Islam—that was based at the time out of [a] refugee camp in Tripoli, in the north of the country, known as Nahr al-Bared. [That group] fought a four-month war with the Lebanese army in the refugee camp, and I think over 400 people were killed in that conflict. After [the Syrian fighters] lost, a lot of the surviving jihadists from Tripoli went back to Syria again. But this time a significant portion of them were angry at the Syrian government for having basically forced them into fighting a conflict on their behalf that they were then abandoned to lose. A good portion of those fighters that went back to Syria started carrying out attacks against the Syrian regime and against military targets. The regime in Damascus put a gag order on state media to not report most of these attacks. But for the first time we saw the arrests of some of these jihadist fighters and commanders. Many ended up being thrown in prison in places like Sednayya in Damascus, in 2007 and 2008. And it was many of those that were released in the amnesties of 2011.

Gilsinan: The use of jihadist militants to advance foreign-policy goals, and then suffering blowback, sounds similar to what Pakistan did in the 1990s, 2000s. I’m sure there are limits to that analogy.

Lister: I’m not a Pakistan expert, but the blowback should have been foreseen. The Assad regime, to many conservative Islamists in Syria, represented something led by Alawites, and if you are a jihadi you see Alawites, and more broadly their Shia allies, as one of the paramount enemies of your transnational cause. And specifically when we’re talking about an organization like [ISIS’s predecessor] al-Qaeda in Iraq, and then the Islamic State in Iraq after that, who had a particularly sectarian worldview, it shouldn’t have been surprising that eventually these guys would turn their guns on their managers. The prisoner releases in 2011 were undoubtedly a cynical attempt to justify the regime’s own claim to be fighting a purely jihadist opposition. But the realization should have been made that eventually this was going to backfire. The manipulation of jihadists doesn’t necessarily mean the long-term management of them.

“The manipulation of jihadists doesn’t necessarily mean the long-term management of them.”

Gilsinan: I’ve heard that claim a lot—that Assad cynically Islamized the opposition through these prison releases. What I always wonder is: Was he really that smart? How do we know what his motivations were?

Lister: We can’t know with 100-percent certainty. But I think if you look at the evidence, a vast majority of people released in both of those prison releases were specifically people who had been detained on Islamist grounds, and a great many of them on militant Islamist grounds. And a vast majority of the people who were not released were just general political prisoners. By almost only releasing Islamists, and at the same time claiming to be only fighting an Islamist opposition—I think that it would be a huge coincidence if this had been done as a conciliatory measure and not as something cynical in order to try and manipulate your enemy into being something that it wasn’t.

Gilsinan: And you also see this, years later, in discussions about the current peace talks—that basically Assad has been trying to maneuver the international community into a position where it has to choose between him and ISIS. Does that mean that his plan working? Or is this worse than he foresaw?

Lister: Well again, this necessitates a rough assessment of how smart or not the Assad regime is. But I think any insurgency expert knows that in any area of the world where religion plays a part in forming one’s sort of social views, the longer a brutal conflict goes on, the more religion will come to shape many people’s view of their specific political cause. I think it was clear that although Syria had been a very cosmopolitan and largely secular country, the roots were there—that if the Assad regime used enough brutality, and the conflict lasted long enough, and enough people were killed, and enough suffering and chaos was created, that the actors on a more conservative and extreme end of the spectrum would become more prominent over time. And moreover, we cannot forget that later on through the uprising, for a significant period of time, the Assad regime refused, basically, to target ISIS in any form, precisely because it was seen as a useful anti-opposition actor, and an effective one at that.

“The Assad regime refused to target ISIS in any form, precisely because it was seen as a useful anti-opposition actor, and an effective one at that.”

Gilsinan: Has the regime’s approach differed according to different groups? So it hasn’t targeted ISIS, but what about groups like [the al-Qaeda affiliate] Jabhat al-Nusra?

Lister: Groups that have demonstrated themselves to be specifically dedicated to the fight against the regime have been consistently targeted, consistently labeled as terrorists, and [have] consistently taken up the focus of regime operations. The ultimate objective of Jabhat al-Nusra is basically no different than that of ISIS. But [Jabhat al-Nusra’s] strategy for getting there is that much longer, that much more patient. They have dedicated themselves solely to fighting the regime and its allies on the ground for the last five years, and for precisely that reason, they are seen as a genuinely existential threat to the regime itself.

Gilsinan: Are there any “moderate” groups any more?

Lister: Yes, absolutely. This is the Middle East, and not the United States, so the frame of reference for assessing someone’s moderation is necessarily different, but with that being said, [up to] 80,000 people still belong to that more conventional, genuinely representative opposition. They want representative government; many of them say they want some kind of democracy. The want equal rights for all, no matter what ethnic or religious minority you might come from, etc. And all of those things are exactly the kinds of expectations that we as the West have sort of placed upon them. The most unfortunate reality for them is that they have not been provided with sufficient support by the international community, [enough so] they don’t feel like they need to use a group like Jabhat al-Nusra as an ally on the ground.

That relationship [with Jabhat al-Nusra] is what has troubled [the moderate rebels] the most, in terms of acquiring further support from the West. And that is the primary reason for why people say, well, these guys can’t be moderate, if they fight alongside al-Qaeda. From sitting thousands of miles away that’s very easy to say, [but] much closer to the ground, the nuance is intensely important.

Gilsinan: That cooperation is not so much about ideology as about survival.

Lister: Yeah, absolutely. These guys are fighting hour by hour to survive, to protect their families, and so they will take every bit of help that they can, just to survive. But the ideological differences between the vast majority of the opposition and Jabhat al-Nusra—those differences are highly significant. And I think we’re seeing some of that play out, literally as we speak. For the first major time, we’re seeing big popular protests rising up against Jabhat al-Nusra in the northwest of the country, in Idlib. That shows that patience with al-Qaeda’s affiliate in Syria is wearing thin.

“These guys are fighting hour by hour to protect their families, so they will take every bit of help that they can, just to survive.”

The consistent line from the opposition and from the civilian people that they claim to represent has been that, we will accept Jabhat al-Nusra’s role in the revolution, so long as it doesn’t begin to contradict our social values and our political objectives in Syria. And I think now, especially throughout the two-week cessation of hostilities, the comparative lack of conflict actually exposed a major weakness in Jabhat al-Nusra, in that it is relying on fighting on a day-to-day basis to prove its credibility to the people. But as soon as that fighting stopped, it very quickly became virtually impotent on the ground, and threatened by the popular protests—people have gone to the streets and are tearing down Jabhat al-Nusra flags from buildings. And that is something we have literally never seen for five years.

It’s a great sign that people have started to stand up against Nusra, but [Nusra has] grown and consolidated and established such deep roots now that it’s very hard to see a scenario where they’re genuinely pushed out from large swathes of territory. So Jabhat al-Nusra will be in Syria for a very long time to come.

Gilsinan: What about ISIS?

Lister: ISIS has much more shallow roots in Syria. I actually think a capable enough force, and one that sufficiently represents the makeup of societies currently under ISIS’s control, could take back a lot of this territory from ISIS relatively quickly. The challenge then will of course be holding that territory and rebuilding it and proving that the [members of that force] represent a better alternative to ISIS control. Which certainly isn’t impossible, but considering the broader situation of chaos in Syria will be a challenge. But Nusra’s deeper roots do lend it a more sustainable presence in Syria than ISIS.

Gilsinan: So do you have high hopes for the current Geneva [peace] process?

Lister: I think no one can deny that the cessation of hostilities lasted longer than people expected. It wasn’t a cessation of hostilities, it was more a dramatic reduction in hostilities, but nonetheless the relative stability that presided over Syria for two weeks was amazing for most people, including myself, who just did not expect this to last as long as it did. I think that that in and of itself is a promising sign—it shows that actors on both sides of the conflict have perhaps more restraint than we expected them to have. Nevertheless, signs from the regime, specifically, in Geneva don’t sound good. They’ve totally rejected any idea of talking about transition and the state of the presidency, which is basically the entire point of the political process.

I guess the one promising sign is that Russia may be considering some element of negotiation with the United States, in terms of finding a mutually acceptable middle-ground solution. So it is possible that in a year’s time, we might be looking at an externally imposed solution on Syria—i.e., the U.S. and Russia mutually agree on a replacement for Assad, and Russia forces Bashar out of the way. But we still seem so far away from that that it’s almost pie-in-the-sky thinking. President Putin’s announcement about the withdrawal of some of Russia’s forces from Syria may, at least in isolation, seem like a positive development, but it all depends on how much of Russia’s forces end up being withdrawn. If you just see a halfway move by Moscow, then almost literally speaking nothing has changed.

Gilsinan: Even in the pie-in-the-sky scenario where you do get some kind of externally imposed transitional government, that doesn’t solve the jihadist insurgency problem, right? We’ve seen, in Afghanistan, that you can have an externally imposed government till the cows come home, and the insurgency’s going to keep going. So what do you think are the prospects for [the talks in] Geneva to actually solve the insurgency problem that we’re talking about?

Lister: This is what I worry about the most. An externally imposed solution will not only not solve the jihadist insurgency problem, but it won’t solve the entire insurgency problem. One percent of the armed opposition may end up accepting an externally imposed solution, but 99 percent will reject it and carry on fighting. So until their demands are met—and the most important one of those is Assad goes, and his replacement is genuinely representative of all of the population’s demands—we will have a significant insurgency on our hands in Syria. And the longer that that state of affairs continues, the more powerful groups like Nusra and ISIS will become, and Nusra in particular. And that’s my biggest fear. Most especially because the international community, and in particular the United States at the moment, seems to be distancing itself more and more and more every week from the idea of meeting opposition demands. Ignoring opposition demands, or subjugating them for the sake of imposing an externally acceptable solution, is tantamount to empowering our enemies in the long term.