In an article in its March issue, the magazine said the Central Intelligence Agency (CIA) and the US military targeted Sabaya, whose real name was Aldam Tilao, and his group after they kidnapped American missionaries Martin and Gracia Burnham and another American Guillermo Sobero in May 2001 holding them for ransom.
"His removal by Philippine forces did not inspire the larger Islamist struggle he had hoped for; the invisibility of the United States’ role reduced the effort to a local police action," The Altantic monthly said.
"In a world where any visible US military intervention prompts a dangerous backlash, Aldam Tilao slipped quietly and permanently under the waves," the article said.
The cover of the magazine shows a camouflaged US soldier peering down a rifle barrel with the caption: "Manhunt Stalking one of Asia’s most wanted terrorists – The Inside Story By Mark Bowden."
The article said the US military enlisted Col. Juancho Sabban, then deputy commander of southern operations for the Philippine Marine corps and his men and supplied them with funds and equipment and just enough quiet technological help to get the job done.
The Marines, running an old-fashioned intelligence operation, were able to recruit Alvin Siglos, a high school friend of Sabaya, to work for them. Siglos was reportedly eager to cooperate because an uncle of his was killed by the bandits.
It was Siglos who supplied Sabaya with CIA-approved essentials such as the backpack, a satellite phone and hamburger and pizza for the Burnhams.
"The food was still hot when it was delivered, registering brightly on the Predator’s infrared," the article said.
It said Sabban’s primary US contact was a CIA officer Kent Clizbee, a big, bald, pale, muscular man "who looked like an American tourist who had taken a wrong turn."
Gracia Burnham and her husband Martin spent more than a year in the Mindanao jungles before a military rescue attempt resulted in Martin’s death and Gracia’s release in June 2002. Sobero was beheaded by the kidnappers earlier during the captivity.
The article said there was competition over who would attempt the rescue.
The American command, with forces in the Philippines for the annual joint exercises, wanted to conduct the raid, using one of its SEAL teams.
The Filipinos reportedly balked at this and squabbled among themselves.
Sabban argued that the Marines not only deserved to conduct the mission but were best positioned and suited for it since his unit had found Sabaya, his men were already in position, and that they counted only 21 armed men guarding the Burnhams.
Army commanders, however, would not be denied. They sent their troops to raid the rebel camp on a rainy afternoon of June 7, 2002.
The article said the Burnhams had just closed their eyes for a nap when the Army struck and gunfire erupted. Martin Burnham was killed in one of the first volleys, shot through the chest. Filipina nurse Edibora Yap was also killed, as were some of Abu Sabaya’s men. Eight of the attacking soldiers were injured.
Sabay himself was able to escape, but left behind his backpack with the hidden beacon.
The article said Sabban was furious about the failed raid. He believed a Marine reconnaissance team headed by Capt. Gieram Aragones would have had a better chance of keeping the three hostages alive if they had been sent in.
On June 20, thirteen days after the botched rescue, Sabaya called his courier Hamja and asked to be picked up from the peninsula for his home islands, the article said.
A few hours later, four boats slipped away from berths at a Navy pier in Zamboanga City and steered north along the coastline.
Two were US Navy vessels, each carrying a SEAL team. Another was the same flat, open, gray wooden speedboat used by Sabaya in kidnapping his victims from the Dos Palmas resort in Palawan. This time the wooden speedboat was carrying Aragones and 15 of his men armed with assault rifles and two M-60 guns mounted at the bow.
Moving well in front of these three was the long, sleek boat christened Kingfisher that its young owner Hamja had for months been using to supply Sabaya. Hamja was snatched by Marines off a street in Zamboanga and wisely agreed to cooperate, the article said.
Tracking everything from above were two CIA pilots in a high-flying RG-8 Schweitzer aircraft. CIA officers watching the monitors in their office in Zamboanga City could see everything.
As the other boats waited just over the horizon, the Kingfisher touched sand and picked up a group of people, the Atlantic article said.
When the RG-8 spy plan passed directly overhead, the CIA officers could see the forms of nine men on board, most of them toward the stern.
The article said the Marines decided to ram the Kingfisher because instead of sailing out to sea, it set its course about a kilometer from shore, close enough to the shoreline for Sabaya and his men to swim to land.
As the speedboat swung around after the collision, the Marines unleashed a torrent of fire at the rebels bobbing in the waves who were also shooting.
The body of one of the rebels in the water was cut in half and vanished under the waves.
Sabaya’s body was never found. But interrogation of four captured Abu Sayyaf men confirmed that the man whose body was cut in half by gunfire was Sabaya’s, the article said.
It said Siglos collected $100,000 reward money promised by the Philippines, but to date has never collected a penny of the $5 million US reward for Abu Sabaya’s capture dead or alive.
A spokesman for the US State Department‘s Rewards for Justice program will say only that Siglos’ case is "under review."