MOMBASA, Kenya—“The state wants to kill me,” the 53-year-old jihadist Abubakar Shariff Ahmed, better known as “Makaburi,” told me in late February. He said he was sure that one day he’d be gunned down by “unknown assailants” on a street in Mombasa. That’s how so many controversial Islamic leaders have died in Kenya in recent months, he said. And then, earlier this week, the prophecy came true.

On Tuesday, “unknown assailants” gunned down Makaburi as he was leaving a courthouse outside Mombasa. Makaburi was waiting by the side of the road along with four other preachers when a vehicle pulled up and sprayed them with bullets. Witnesses reportedly saw Makaburi’s body, swaddled in a white kanzu, or robe, lying partly in a ditch. His colleague Sheikh Bohero also was killed.

Young men in the neighborhood told a local reporter that the two shooters were dressed in white kanzus, too, suggesting they were Muslims, and perhaps known to Makaburi and the others. But few in Kenya credit that possibility. The record of murders in recent months provides ample indication that a dirty war is being waged. Its evident purpose is to exterminate and intimidate people believed to be associated with the Al Shabaab movement in neighboring Somalia. For several reasons, those carrying it out may believe they have at least the tacit support of the United States, and, as often happens with dirty wars and death squad operations, this murderous campaign appears be galvanizing the opposition it aims to destroy.

Makaburi (the nickname means grave digger in Swahili) preached at the Musa mosque in Mombasa, which is considered an incubator of radicalism, and Makaburi recruited fighters there for Al Shabaab, which has developed close ties with Al Qaeda. On Sunday, February 2, security forces raided the mosque for hosting what the police described as a “jihad convention.” They stormed the building, firing tear gas and live rounds in a raid that resulted in 129 arrests and eight deaths, including that of a policeman. Before that, two other clerics associated with the place had died in a hail of bullets.

When Makaburi and I talked in February, he claimed that the others had been “assassinated” in “retaliation” for last year’s attack on Nairobi’s Westgate shopping mall, in which members of Al Shabaab claimed responsibility for killing at least 67 civilians and injuring hundreds. But the killings started before that, as one radical imam after another has been murdered or disappeared. Religious leaders say Kenyan security forces are targeting them unfairly for persecution if not indeed for summary execution, but the police argue they have clear intelligence linking many of the local preachers to Somali terrorists.

Makaburi told me when I saw him that he thought the only reason he was still alive was that Kenya feared domestic unrest. Some of the “unknown assailant” murders have led to bloody rioting. But whoever killed him seems to have thought the risk worth taking, and days after the shooting the reaction is still muted.

On the day we met, Makaburi was as welcoming and relaxed as he could be. Our three-hour interview took place in his cockpit-sized apartment in Mombasa’s run-down Majengo district, which has been the epicenter of recent violence. Around him he’d arrayed a desktop computer, a wall-mounted plasma TV with images of Muslims he said the police had tortured, miniature copies of the Qur’an, and a few creature comforts: an industrial-size bag of mini chocolate bars, and tubs of Blue Band margarine.

Behind Makaburi’s head was pinned a black flag with the profession of faith, the shahada, written on it: “There is no God but God and Mohammed is his messenger” and, beneath it, a single primitively drawn sword.

“Don’t worry, I am not going to suck your blood,” Makaburi assured me. I’d been struggling to cover my hair with a scarf to use as a hijab. He asked if it were bothering me. “Don’t wear it if you don’t want,” he said. “Pretending to be something you’re not is disrespecting yourself. Just be yourself.”

The genial imam made an interesting contrast with the image of him painted by the United States, the United Nations and Kenyan authorities.

A 2012 U.S. Treasury report blocking the assets of several people suspected of supporting Al Shabaab closely mirrors language also adopted by the United Nations Security Council (PDF), and it reads like a ringing indictment of Makaburi:

“He provides material support to extremist groups in Kenya and elsewhere in East Africa. Through his frequent trips to al-Shabaab strongholds in Somalia, including Kismaayo, he has been able to maintain strong ties with senior al-Shabaab members,” the U.S. report said. Makaburi “also engaged in the mobilization and management of funding for al-Shabaab,” he “has preached at mosques in Mombasa that young men should travel to Somalia, commit extremist acts, fight for al-Qa’ida, and kill U.S. citizens.” He was “a leader of a Kenya-based youth organization in Mombasa with ties to al-Shabaab” and “acted as recruiter and facilitator for al-Shabaab in the Majengo area of Mombasa.”

Some of the accusations, Makaburi told me, “are bullshit—like ‘committing extremist acts’ and ‘financing terror.’” He pulled out a desk drawer and removed a few filthy currency notes. “This is all I have—640 Kenya shillings,” which would be less than $10. “I don’t have enough to fund a reporter, let alone a terrorist organization.” But then he went on. Some of the accusations “are correct,” he said. He made no apology for recruiting young men to wage jihad in Somalia.

"Radicalizing the youths is the only direction to go when the Kenyan government won’t allow the constitution to protect them and when police are killing sheikhs and imams extrajudicially,” said Makaburi. “Are we supposed to take this lying down?”

The accusation that Makaburi encouraged young men to kill Americans touched a nerve—and did not elicit a denial. “Let me ask you,” he said, “Americans are invading other people’s lands, taking them prisoners, renditioning them and torturing them. Raping and killing innocent women and children is not allowed in warfare.” The argument is boilerplate Al Qaeda, but many people in developing countries, Muslims and non-Muslims alike, find it persuasive.

When the post-9/11 Global War on Terror waged by the Bush administration was at its height, Kenya became an important player in American eyes. Since 2003 Kenya has received extensive aid from the State Department’s anti-terrorism assistance fund and a program now known as the Partnership for Regional East Africa Counterterrorism, or PREACT. Among its objectives, according to the State Department, “It uses law enforcement, military, and development resources to achieve its strategic objectives, including reducing the operational capacity of terrorist networks.”

Things intensified when Kenya invaded Somalia in 2011 in an operation called Linda Nchi (Swahili for “Protect the Country”), ostensibly in reaction to kidnappings of tourists in northern Kenya. It was considered inevitable that Al Shabaab would try to strike back on Kenyan territory.

Al Shabaab’s ideological and military leaders regrouped and began recruiting Kenyans to fight in Somalia and build support in Kenya. This was where Makaburi’s work became important.

The July 2012 U.N. report on Shabaab-related activity identified a homegrown Kenyan group called al-Hijra under the leadership of the charismatic Sheikh Aboud Rogo and Makaburi. After those published reports a growing number of clerics and imams were killed or—in human rights parlance—“forcefully disappeared.”

In May 2012 blind cleric Mohammed Kassim and fellow hardline cleric Samir Khan were traveling to Manjengo when men in a white Toyota van stopped them by the side of the road. The pair had been charged with possession of illegal firearms and recruitment of youths to Al Shabaab, but not convicted, just the kind of situation that tends to precede extrajudicial killings. Khan’s mutilated body was found in Voi, some 150 miles from Mombasa. Kassim’s body has not been found, and if he is alive his whereabouts are unkown.

On August 27, 2012, one month after the U.N. report was published, “unidentified assailants” gunned down Rogo as he drove his wife home from a Mombasa hospital. Weeks before his assassination the sheikh had contacted human rights groups saying that he feared for his life, but they were unable to help him. Rogo’s death sparked days of rioting in Mombasa. Young men took to the streets, hurled grenades and burned churches.

“It’s difficult to say who killed Rogo,” says Jonathan Horowitz, the legal representative with Open Source Foundation’s National Security and Counterterrorism Justice unit, funded by philanthropist George Soros. “But when you look at circumstantial evidence, the pattern of events, the modus operandi, and the audacity with which the killing took place, it all points to the hand of the state.”

After Rogo died, Makaburi was his natural successor. “He was more than a brother to me,” Makaburi told me, and Makaburi was outraged at what he regarded as a US-government-funded extermination project:

“I am the one who is accused of radicalizing when it’s the police who are radicalizing the Muslim youth by killing us.”

Meanwhile, Al Shabaab and its allies have not remained passive. The Westgate Mall attack commanded global attention day after day last September, but it was part of a much wider pattern of violence. According to the report “Kenya and the Global War on Terror” issued by the London School of Economics, “Shabaab and its sympathizers have conducted more than 50 separate grenade attacks in Kenya, believed to be in retaliation for Operation Linda Nchi and more widely the foreign policy of Kenya.”

Most of the extremist attacks have occurred in northeastern Kenya near the Somali border. But the violence made headlines again in November last year when two grenade attacks occurred in Diani, a tourist resort town south of Mombasa. On December 12 police said a grenade was hurled at a minivan carrying two British tourists. The grenade never exploded and the tourists were unharmed.

On January 2 a grenade exploded in a sports bar in the same tourist town and authorities labeled it a “terrorist attack.” There were no fatalities in either incident but they were widely reported in the international media.

The tit-for-tat violence grew increasingly brutal. On December 3, the headless body of Faiz Rufai, a former Shabaab member and madrassa teacher believed to have turned informant, was discovered washed ashore on a remote beach up the coast. Al Shabaab “sympathizers” allegedly carried out the beheading and posted a camera-phone video of the decapitation on Facebook.

Word went out in jihadist circles that Rufai’s handler in the security services was Athmed Bakshwein, a 61-year old police reservist, who was also said to have played an important role in other terrorist cases. On January 28, Bakshwein was gunned down in broad daylight as he was parking his car in front of a hardware store in his hometown of Malindi.

Leaflets circulated in Mombasa featured the image of Bakshwein’s bullet-riddled corpse and called him a traitor to Islam. “Supporters of jihad have begun killing informers,” proclaimed the flyer. “It is a sign that jihad is not far. … May Allah clean the mosque of informer imams and traitors and finish them one by one.”

The Kenyan police assault on the “jihadist convention” at the Musa mosque came just days later.

When I met with Makaburi to discuss all this, he was defiant. “I challenge Obama to give me my day in court anywhere in the USA to prove that I am financing Al Shabab. I am willing to travel today,” Makaburi told me.

Makaburi never got his day in a US court. But at the time of his death Makaburi had several cases against the police pending in Kenya. Last week, days before he was gunned down, the high court awarded him $7,718 in damages for the violation of his rights when police raided his house in 2011.

The violence continues to mount. Last month armed men attacked a church in Likoni, leaving eight people dead, including a young boy. Since then Kenya has asked the United States for more funding to combat terror. U.S. Ambassador Robert F. Godec said that recent sporadic violence in Mombasa was a sign that terrorism in Kenya was a real threat and vowed to stand by Kenya’s side. In a statement issued this week Godec said the United States “deplores the recent violence on the Kenyan coast,” including the murder of Makaburi, and called for “calm and restraint.” He also called for the Kenyan government to “undertake full investigations” of the “murders” of the Muslim clerics and the “terrorist attack” on the church. Those responsible, he said, should be held accountable “through the Kenyan justice system.”

In response to questions from The Daily Beast about the impact U.S. aid has on Kenyan counter-terror operations, Godec said “all training includes modules devoted to respect for human rights and the rule of law.”

But Horowitz’s summation of the situation is probably more realistic. “Groups that subscribe to violent extremism often justify their actions by citing the government’s human rights abuses, including extrajudicial executions,” he said after Makaburi was gunned down. “But the Kenya government has a lot to answer for… Ending these murders and ending violent extremism in Kenya are inseparable. The Kenyan government has failed to grasp this.”

When I met with Makaburi in his little apartment, he seemed completely resigned to his fate. He had been born in Mombasa and brought up there. His father, who worked in a box factory, was fixing a fan one day at home and got electrocuted. “He died when I was a child still crawling,” said Makaburi. Death happens. Life has strange twists. As he and his brothers grew up they took different paths. In fact, one of his brothers works for the Kenyan intelligence service, he told me. “Sheik Rogo used to say my mother was fair: she gave one son to Obama and the other to Osama.”

Then Makaburi said, simply, “I am waiting to be killed.” And so he was.