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The Secret War: Fourth in a series

This series is the result of a six-month investigation by Army Times senior staff writer Sean D. Naylor. Naylor reached out to dozens of current and former diplomatic and military leaders and special operators about their activities in the Horn of Africa. It is a war few will acknowledge and even fewer will discuss. Nevertheless, Army Times was able to piece together a mosaic that shows the level of involvement by U.S. forces in Africa and the significant resources that have been employed — with mixed success — to hunt terrorists in Africa. • Read parts 1-3

His tour over, John Bennett was preparing to fly home. The CIA's station chief in Nairobi, Kenya, Bennett had been running the United States' secret war in East Africa, negotiating with Somali warlords while hunting al-Qaida members across the region. On his watch, the United States and its proxies had managed to capture or kill at least 10 or so al-Qaida militants.

ID=78535586 However, the most wanted al-Qaida figure in East Africa, who went by a variety of aliases but whom U.S. officials called Harun Fazul, was still on the loose. A native of the Comoros Islands wanted in connection with al-Qaida's 1998 attacks on the U.S. embassies in Nairobi and Dar es Salaam as well as the November 2002 attacks on Israeli targets in Kenya, Fazul had proved "a very savvy" enemy, according to an intelligence source with long experience in the Horn of Africa.

As Bennett made final preparations for his flight out of Kenya the evening of Aug. 1, 2003, his officers and Kenyan authorities were keeping tabs on an Internet café 274 miles to the southeast, in the city of Mombasa, where someone using an email address the CIA associated with al-Qaida in East Africa had been logging on. "There was a pattern of communications, so they were kind of on standby," the intelligence source said. "The pattern was the date, time and location at which somebody was accessing the Internet."

"Clearly, it was a favorite spot of somebody's," the source said.

Bennett had a case officer in Mombasa coordinating with the local police, the source said. That case officer was present when the Kenyan authorities arrived at the café to arrest the suspected al-Qaida emailer, only to find two suspects — both male, one larger than the other — instead of one. With the case officer on the phone with the Nairobi station reporting events in real time, the police placed both under arrest and were about to put them into a paddy wagon when the larger suspect, later identified as a young Kenyan named Faisal Ali Nassor, suddenly gave his companion a sharp shove and then pulled a grenade from his clothes. "One guy pushes the smaller guy away from him," said a special operations source with firsthand knowledge of operations in the Horn. "The [larger] guy blows himself up and takes the police out."

The explosion killed Nassor and a policeman. In the ensuing chaos, the other suspect made a run for it. To the surprise of the CIA and the Kenyan authorities, that man turned out to be Harun Fazul, East Africa's most wanted man with a $5 million bounty on his head. "Clearly we didn't expect to get Fazul himself," the intelligence source said. "We figured we'd get just his courier."

But rather than just being a courier, Nassor was "a suicide bodyguard," said the special ops source.

Security forces converged on the scene, but Fazul was too smart for them. He ran into a mosque and emerged disguised as a woman, wearing a hijab or some other form of Islamic facial covering. "He walked right out as a woman and nobody touched him," the intelligence source said.

Fazul had moved in with Nassor that July. Using an ID seized from one of them, the security forces went straight to their apartment. There they found Fazul's passport, a machine for making visas, "bits and pieces of other passports," as well as a light anti-tank rocket hidden in a couch, said the special ops source. But of Fazul himself, there was no sign. The wily operative had again given the authorities the slip. It would be another eight years before Fazul's tradecraft — and his luck — would fail him.

The search for Fazul typified much of the U.S. man-hunting campaign in the Horn: It combined CIA and special operations personnel (often working through local forces), high-tech gear alongside low-tech human intelligence skills and raw courage. And yet it was often characterized by frustration and near-misses.

For sheer drama, Fazul's escape with the help of his "suicide bodyguard" was rivaled by a similar disappearing act he pulled off a year earlier. On July 12, 2002, Kenyan police picked Fazul up in a Mombasa shop for purchasing jewelry with a credit card stolen during an armed robbery. But, according to a June 2004 Associated Press story, the cops had no idea of his true identity.

The next day, seven armed police officers took Fazul to what they thought was his apartment, hoping to find stolen goods. Instead, they discovered three women and a mentally handicapped man yelling at them. Fazul, who was not handcuffed, took advantage of the chaos to sprint out. "The man was well-trained, I tell you," one of the police said. "He dashed to the door like a monkey, then, like a flash, he slides down the stair rail like lightning." Fazul ran out and lost his pursuers in Mombasa's narrow streets.

Four months later, Fazul allegedly was a key participant in al-Qaida in East Africa's Nov. 28, 2002, twin attacks in Mombasa: the truck bombing of the Israeli-owned Paradise Hotel, which killed about 15 civilians, and the firing of two SA-7 man-portable anti-aircraft missiles at an Arkia Airlines Boeing 757 as it took off carrying 261 passengers bound for Israel. (Published reports said both missiles missed the plane, but the special ops source said a missile went through the tail without exploding.) No one was hurt.

Another near-miss in the hunt for the cunning al-Qaida operative occurred in the first half of 2003 during an operation in northeastern Kenya by Joint Special Operations Task Force - Horn of Africa, which fell under Combined Joint Task Force - Horn of Africa, based in Camp Lemonnier, Djibouti. JSOTF-HOA's search for Fazul, Operation Bowhunt, was a mission to develop intelligence and was "completely separate" from Operation Black Hawk, the CIA hunt for the members of al-Qaida in East Africa, according to the special ops source. "The other fellows [the CIA] were only going up north [i.e., into Somalia]. They weren't spending a great deal of effort down south [i.e., in Kenya] at all."

Key to Bowhunt was the high-speed vessel Joint Venture, an Australian-built catamaran designed for shallow-water access and leased by the U.S. military. JSOTF-HOA used it to probe the islands near the Kenya-Somalia border, looking for "the number-one HVT [high-value target]," as the source described Fazul.

"They actually met [Fazul's] wife down on one of the islands," but her husband slipped the net again, said the source. "They missed him by 24 or 48 hours."

Throughout the rest of the decade and into the next, as his colleagues in al-Qaida in East Africa and their local allies died in U.S. air and missile strikes or in combat with Somali Transitional National Government security forces or Ethiopian invaders, Fazul's status — and his legend — only grew. He escaped another dragnet Aug. 2, 2008, when dozens of Kenyan police raided a house in which he was believed to be staying in the coastal town of Malindi. The cops found two non-Kenyan passports bearing Fazul's photograph and a computer that had not been turned off, but the al-Qaida man was nowhere to be seen, according to the Kenyan newspaper The Daily Nation.

The following year, Fazul took command of al-Qaida in East Africa. In a speech in the Somali city of Kismayo marking his appointment, he vowed to spread jihad to Somalia's neighbors. "Praise be to Allah, after Somalia we will proceed to Djibouti, Kenya and Ethiopia," he said, according to a translation posted on the Long War Journal website.

When it came for Fazul earlier this year, the end was sudden, violent and completely unexpected. Late on the night of June 7, troops loyal to the Somali government (which controls little territory outside Mogadishu) stopped a black Toyota SUV carrying Fazul and driven by another militant, Musa Hussein, at a checkpoint on the outskirts of the Somali capital. When Hussein produced a pistol and reportedly fired a round, the government troops shot back, killing both militants. The Somali authorities did not initially realize they had killed Fazul, who was reportedly carrying a forged South African passport, $40,000, laptops and telephones, and buried the two militants quickly, before exhuming the bodies and comparing them to photos of Fazul.

Most published reports described the incident as simply the result of Fazul and Hussein getting lost, but a detailed account on said Fazul was set up by Ahmed Abdi Godane, the leader of al-Shabaab, a Somali Islamist militia allied with al-Qaida.

Godane had learned that senior al-Qaida figures had lost faith with al-Shabaab's Somali leaders, who they blamed for recent defeats by Somali government and African Union forces. Fazul's mission was to effect this change, replacing Godane and other Somalis with foreign leaders, according to, which attributed the information to al-Shabaab intelligence officials and other sources. Godane directed Fazul and Hussein to an al-Shabaab checkpoint. He then ordered the fighters manning the checkpoint to break it down and abandon the position, meaning that when Fazul and Hussein, neither of whom knew the area well, arrived, they continued down the road, running into the government checkpoint as Godane had planned.

This account would explain why, when first stopped at the checkpoint, Hussein told the soldiers the car was carrying "the elders," an honorific term for al-Shabaab leaders, according to an AP interview with the soldier who stopped the vehicle. That comment, indicating at least two passengers, along with the fact that, in the aftermath of the incident, one of the SUV's rear doors was found open, also suggests that there might have been a third militant who escaped.

The United States has been monitoring cellphone conversations in Mogadishu since at least the 2003-2004 time frame but had no role in Fazul's death, according to a senior U.S. intelligence official. "It would have been a much better ambush had it been planned," the official said. "Had it been set up, nobody would have gotten away, they might even have captured him."

When the Kenyan police arrested Fazul in the Mombasa store in July 2002, they also took a man pretending to be his taxi driver into custody. That man was a 23-year-old Kenyan named Saleh Ali Saleh Nabhan, a senior al-Qaida in East Africa figure. Not realizing his value, the police allowed him to post bail, after which he promptly disappeared. The United States had been tracking Nabhan since early 2002, according to the intelligence source with long experience in the Horn. But after Nabhan reunited with Fazul — four months after skipping bail — and conducted the Mombasa attacks, finding him and the others connected to the incidents became a U.S. priority.

To crack the Mombasa case, U.S. investigators proceeded from "an assumption" that the militants had used cellphones, based on the attacks being "two near-simultaneous events relatively close together, geographically — probably no more than 20 miles apart," the intelligence source said. The next step was to get the records of all the cellphone calls made during the period just before the attacks and determine "all the numbers that never made a call again," the source said. In addition, investigators "went back and looked at where they bought the scratch cards and where they bought the phones," he added.

It took "a few months" for U.S. intelligence agents to figure out which cellphone numbers were associated with the attackers, the source said. The key to the breakthrough was the militants' sloppy tradecraft: One of them was apparently given money to buy two sets of phones and SIM cards, but figured he could keep some cash for himself by just buying one set of phones, mistakenly thinking that switching out the SIM cards provided enough operational security. "They used the same phones but different SIM cards," the source said. "They didn't understand you could track the phone too."

Israeli intelligence agents also gave the Americans a lot of information and asked the U.S. agents to work with them, the source said. "The Israelis were key initially," the source said. "Clearly, they had their own sources in the region."

The Kenyans also conducted "some very good investigative work," the source said. "They were brought in and made to feel like they were valuable." The Kenyan authorities used information provided by U.S. intelligence to get the lower-level al-Qaida operatives involved in the attacks. "They made some arrests," the intelligence source said. "That was all U.S.," the source said of the intelligence that resulted in the arrests. Col. Mike Garrison, then the U.S. Defense and Army attaché to Kenya, ended up with the expended SA-7 launcher tube from the airport attack, the source added. (Garrison declined to be interviewed for this story.)

But Nabhan got away. "He was very clever; he understood how to communicate under the radar," the source said."

One way Nabhan evaded his enemies for so long was by "rarely" communicating himself. "He'd send a message with somebody [and] they'd go to an email or hotmail account and send that message," the source said. Al-Qaida in East Africa used a very basic "10 code" when passing on numerical information, the source said. The code involves replacing each digit with the number that would be required to bring the replaced number up to 10 — for instance, they'd write 539 instead of 571. "It's really simple, but it took people a while to figure out they were doing it," he said.

Perhaps aware of the growing U.S. ability to monitor their cellphone conversations, al-Qaida cell members switched much of their conversation to the Internet, the source said. But they didn't change their email addresses often enough, allowing U.S. intelligence to track them, the source said. Eventually, "we were able to find ways to break into" Nabhan's communications, the source said.

Pushing particularly hard for the authority to go after Nabhan was Joint Special Operations Command, the organization that conducts the military's most sensitive special operations. (Units that fight under JSOC include the Army's 1st Special Forces Operational Detachment- Delta, also known as Delta Force; the Naval Special Warfare Development Group, also known as DevGru and SEAL Team 6; and a special mission unit based at Fort Belvoir, Va., often known as Task Force Orange, which specializes in gathering human and close-in signals intelligence.)

Between 2001 and 2004, JSOC never had more than three people at a time in Somalia, according to the intelligence source. During the latter part of that period, those operators were supporting CIA missions in Mogadishu to liaise with Somali warlords and install cellphone monitoring equipment, the source said.

JSOC was the junior partner on the first Mogadishu missions, but its strength in the Horn was slowly expanding. During those early years, Orange provided the core of JSOC's presence in the region, including personnel assigned to the U.S. Embassy in Nairobi as well as a few in Camp Lemonnier, Djibouti, who functioned as liaisons to CJTF-HOA. In mid-2003, an "interagency node" staffed with intelligence and law enforcement personnel was established in the Nairobi embassy under JSOC auspices, said a special operations officer. Manned at first by "maybe six" people, it quickly grew and now has about 20 people, the intelligence source said.

This reflected the growth of JSOC's wider presence in Kenya. The command started out with three people in Nairobi, a number that grew to five or six and now is reputed to be in the "scores," the source said. "The writing was on the wall that eventually this was going to become a DoD-centric effort," he added.

JSOC's effectiveness in the Horn "really ramped up in the 2004-2005 time frame," when it "doubled" its resources in Kenya and focused more tightly on intelligence collection and target development, the senior intelligence official said. As a result of JSOC's efforts, "we gained a lot of understanding of what was going on," the official said.

The elite command continued to "thicken" its network in the Horn, a process that included placing a small team in the Ethiopian capital of Addis Ababa, according to the intelligence official. JSOC commander Maj. Gen. Stanley McChrystal also began conducting Horn of Africa-specific video-teleconferences that connected U.S. ambassadors and CIA chiefs of station in the region with officials in Washington, the official said.

In 2006, JSOC began to run its own operations in Somalia, a senior military official said. At the time, the JSOC task force in the Horn was called Task Force 88, but that has since changed, sources said. The task force was headquartered in Nairobi, but also operated out of a small base at Manda Bay in northeastern Kenya, about 50 miles from the Somali border.

Some in the intelligence community wondered whether JSOC and, by extension, its Defense Department bosses, were too focused on Nabhan. "I think there was a fixation certainly at DoD," said the intelligence source, adding that while some intelligence personnel thought "that a movement doesn't really center on one person," JSOC saw the Nabhan hunt as a way to validate the mission it was trying to carve out in non-combat theaters. "JSOC saw Nabhan as a way to shore up that third leg of the stool," the source said.

The United States and its regional allies hunted Nabhan for the rest of the decade. "There were several times we've gotten close to him," said the special operations officer, adding that he meant "close" in terms of surveillance, not missions to kill or capture the al-Qaida figure. Meanwhile the JSOC operators chafed under what they viewed as political restrictions that prevented them from going after Nabhan.

But on Sept. 14, 2009, they were given the green light. "We'd been tracking him for years," the senior military official said. Finally, according to the official, JSOC had both human and signals intelligence leads on Nabhan's location as he joined several other militants in two vehicles to make the 300-mile trek from Merka to Kismayo in southern Somalia. "We knew his travel route, we knew the vehicles he was using," the official said.

When the convoy was near the coastal town of Barawe, JSOC struck. Multiple 160th Special Operations Aviation Regiment AH-6 Little Bird helicopters flew ashore from a Navy ship and attacked the militants as they were breakfasting, killing six, including Nabhan, according to news reports. One helicopter landed and operators jumped out and loaded the bodies of Nabhan and three others into the aircraft.

The Associated Press contributed to this report.