AS THE SOMALI LEADERS of al Shabaab have moved to reassert their authority, al Qaeda, along with the foreign fighters, has found itself marginalized.

Osama bin Laden had always wanted to establish a foothold in Somalia for al Qaeda. But the country’s clan-based system made that very difficult. The Ethiopian invasion and U.S. killing campaign had changed that. Bin Laden named Mohammed Fazul, a Comoros-born al Qaeda operative, as a head of al Qaeda in East Africa with a major directive to support the jihad in Somalia. Fazul was one of the masterminds of the 1998 U.S. Embassy bombings in Kenya and Tanzania and had organized a series of attacks against Western targets in Kenya in 2002.

Abdirahman “Aynte” Ali, a leading scholar on al Shabaab, told me that Fazul served as “the bridge between al Shabaab and al Qaeda, tapping into the resources of al Qaeda, bringing in more foreign fighters, as well as financial resources — more importantly, military know-how: how to make explosives, how to train people, and so on. So that’s when they have gained the biggest influence that they needed.”

In August 2010, al Shabaab declared what it called a “massive war” against AMISOM troops, which at the time numbered some 6,000. They hit convoys, deployed suicide bombers and attacked government ministers, sowing fear and terror and seizing some territory in Mogadishu. The U.S. and other Western nations began beefing up support of the besieged peacekeeping force, which led to an overwhelming offensive — complete with indiscriminate shelling of Shabaab positions — and ultimately forced Shabaab into what the group tried to characterize as a strategic retreat. Shabaab had taken heavy losses, and its leaders began to bicker over the group’s next steps.

By 2011, Fazul Abdullah Mohammed’s world had grown very small. Almost all of his East African al Qaeda comrades had been assassinated by JSOC, and he lived life on the run. He had a $5 million bounty on his head, courtesy of the U.S. government. Some intelligence reports indicated that he may have had plastic surgery, and there were periodic reports of him popping up throughout the Horn of Africa using aliases and fake passports. With many of the veteran al Qaeda leaders gone, Fazul was increasingly isolated and dealing with the complexities of Somalia’s clan politics. Then, on May 2, Osama bin Laden was killed.

Fazul was finding it more and more difficult to deliver adequate resources from al Qaeda to al Shabaab, and al Shabaab sought out different means of financing and support, including making deals with powerful clans.

So Fazul found himself at odds with al Shabaab’s Somali leadership. I interviewed a Somali intelligence source who was given access to some of Fazul’s writings seized by his agency in 2011. They described growing “fissures,” revealing that “Fazul thought, essentially, that al Shabaab is going the wrong way, that the traditional warfare that’s going on between al Shabaab and the government was not sustainable anymore.” Fazul alleged that al Shabaab was recruiting young people, but then “in a few months they’re just sending them as suicide bombers. And he thought that was such a bad idea, and that in the long run it would just erode fighters out of al Shabaab.” The source added: “I mean this guy’s looking way ahead, and he’s accusing the al Shabaab leadership of being shortsighted.”

On June 7, 2011, Somali intelligence operatives informed the CIA that Fazul had been killed by some local militiamen in Somalia. Fazul, they said, had taken a wrong turn, had an altercation with the soldiers at a checkpoint and was gunned down. The Americans, the Somali intelligence official told me, were “unbelievably grateful.” Then-Secretary of State Hillary Clinton called Fazul’s death “a significant blow to Al Qaeda, its extremist allies and its operations in East Africa. It is a just end for a terrorist who brought so much death and pain to so many innocents.”

Neither Ibrahim nor the source with close ties to al Shabaab interviewed for this story believe the official version of events in Fazul’s death. They suspect that Fazul was assassinated, not by militiamen or by the CIA, but rather by al Shabaab. “At that time, the former leader of al Shabaab, Abu Zubayr, and Fazul, they kind of had some kind of clash,” says Ibrahim. “I’ll be killed by Shabaab soon. If I am killed, don’t waste my blood,” Ibrahim says Fazul told a senior Somali Shabaab leader who supported the foreign fighters. “The conflict continued until this assassination happened. I think al Shabaab planned that assassination. I don’t think it was a mistake. I think it was set up,” says Ibrahim.

IN THE MONTHS after Fazul’s death, the fissure between the local Shabaab leadership and the foreign fighters widened. Omar Hammami began openly criticizing the Shabaab leadership’s tactics and decisions. “He never accepted any kind of humiliation and disrespect, and basically he stood up for his rights,” says Ibrahim.

The source with close ties to al Shabaab told me that during Hammami’s conflict with Shabaab’s leadership, Hammami would, at times, walk around with a suicide vest on. The message: if you try to kill me, you will go down with me.

Hammami and other leading foreign fighters forged an alliance with Mukhtar Robow, a longtime senior member of Shabaab. That’s when the internal civil war for control of Shabaab exploded. Shabaab began an assassination campaign against prominent foreign fighters and their Somali allies, several of whom were wanted by the U.S. or designated for kill or capture by the CIA. In June 2013, they killed Sheikh Moalim Burhan and Ibrahim Afghani, a Somali who had lived in the U.S. in the 1980s. “Those guys somehow they wanted to start some kind of small revolution, and some kind of uprising. They tried to speak publicly,” says Ibrahim. “They took them out in Barawe, killed them both.”

Robow, who also had a $5 million bounty issued by the U.S., and another Shabaab leader publicly denounced Shabaab’s chief, Abu Zubayr. Robow accused the Shabaab leader of ordering the killings of top foreign fighters and of plotting to kill Hammami, calling it “a big crime against the blood of our brothers.”

That month, Robow fled Shabaab-controlled territory and returned to the safety of his family’s stronghold. “He felt like he wasn’t safe, so he ran away to Bakool, where his family stayed and he’s under protection by his clan now,” says Ibrahim.

When Robow left, Hammami lost his most powerful protector. He began live-tweeting Shabaab’s attempts to kill him, at one point posting a picture of what he claimed was a wound from a would-be assassin’s bullet that had grazed his neck. “Just been shot in neck by shabab assassin. not critical yet,” Hammami tweeted in April 2013. Later he alleged that Shabaab was sending in assassins from various directions: “abu zubayr has gone mad. he’s starting a civil war,” he tweeted.

Eventually, on September 12, 2013, Hammami was killed. Long sought by the U.S. government, his killers were not from the CIA or JSOC, but al Shabaab.

“The foreign fighters made [Shabaab] go forward. And one of them was Abu Mansour al Amriki [Hammami]. He played a big role, he was a very smart guy, he improved a lot of things,” recalls Ibrahim. “He made Shabaab be more international. The Shabaab killed him, man. That’s clear cut because the guy became a public threat.” Hammami was killed alongside his friend and fellow foreign fighter — a British citizen who went by the name Osama Pakistani.

As Ibrahim watched Shabaab implode and witnessed his fellow foreign fighters imprisoned or assassinated, suspicions that had lingered in the back of his mind began to dominate his thoughts. He realized he had made a life-altering and potentially life-ending mistake in coming to Somalia. The story could end, not with his dying in jihad, but in being killed or imprisoned by his former allies from al Shabaab.

Some of Ibrahim’s colleagues have been killed, while others have disappeared in secret prisons run by Shabaab. Their imprisonment is often preceded by an allegation of spying or conspiring against the Shabaab leadership. “They had secret prisons before, but the secret prisons became more effective after the killings of Abu Mansour al Amriki and Sheikh Burhan and all those guys,” he says. “Whoever goes against Shabaab, says anything they don’t like, they will be seen as an enemy to the Shabaab and somehow they will hit you [because] you are not serving their interest. You’ll see yourself missing, in an underground prison being tortured.”

What kind of torture?

“Beatings, waterboarding, they used some kind of gas. They tie you up for hours and hours. Lack of food, lack of sleep. You might be whipped outside, nighttime. You might be crucified, tied to a car. Tied to the back of an SUV [that they] then drive. All these types of things.”

Most of the people in the prisons, Ibrahim says, are foreign fighters, including, at present, at least two Americans. “Most of the time what they do is they will categorize you as a spy and will have you locked up in an underground prison,” he says. “You know you might be serving over a year and when you come out then you might have two options: to keep quiet or otherwise you’ll be deported.” Deported, he says, means being sent to a country that would likely charge you as a terrorist for being a member of al Shabaab, as the U.S. has done repeatedly.

It could also mean being dumped on the streets of Mogadishu. The Somali government has started an amnesty program for Somalis who leave al Shabaab. If they turn themselves in, they will have their freedom. But it comes with the risk of assassination by Shabaab.