Odyssey into the Shadows: Jose Padilla Was on the Move, but His Alleged Mentor, Abu Zubaydah, Was in Custody in a Secret Location-And Talking. A Glimpse Inside the Underground War

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Byline: Mark Hosenball, Michael Hirsh and Ron Moreau

It was the usual transatlantic flight: nine hours of fidgeting to get the pillow right, first-run movies flickering mutely on small screens, an indigestible flow of starchy food and drinks. Bound for Chicago from Zurich on the morning of May 8, the passengers of Swiss International Air Lines Flight 8 saw nothing amiss. Certainly they didn't know they were on the front lines of a global war being waged under their drooping eyes. But the crew knew it. They had been warned that a major terrorist suspect was scheduled to fly on the plane, according to an official of the Swiss airline pilots union. And a scattering of very wakeful men in nearby seats knew it: they were actually a small squad of FBI agents and a separate team of Swiss Special Forces commandos, all carefully positioned around the suspect, all warily watching his every move. For nine hours.

This airborne stakeout was directed at one Jose Padilla, a.k.a. Abdullah al-Muhajir, a Brooklyn-born street thug now identified by investigators as a would-be Qaeda terrorist. After moving mysteriously for a month from Karachi to Zurich to Cairo and back to Zurich--the kind of city-hopping we've come to associate with a Qaeda plot--Padilla was headed back to his homeland to wreak havoc, or possibly just scout out a good target, U.S. authorities believe. Padilla allegedly was one of the band of foreign terrorists who, as the Taliban fell late last year, had escaped into Pakistan with Abu Zubaydah, a senior deputy to Osama bin Laden. Tipped off by Zubaydah--who was arrested in Pakistan in late March and has since been relentlessly interrogated in a top-secret location--authorities had recently connected a fresh pair of very alarming dots: they had pieced Padilla's name together with vague allegations from Zubaydah about a "dirty bomb" plot, possibly aimed at Washington, D.C. Even so, the Feds were lucky. Though Padilla came to their attention back in March, U.S. intelligence officials say they did not realize how dangerous he was until weeks after he took off on his trip, and for more than a month they had no firm fix on his whereabouts, NEWSWEEK has learned. Only a last-minute search of itineraries of thousands of passengers known to be traveling toward the United States had turned up Padilla's name--less than 48 hours before his flight to Chicago.

FBI bomb and hazardous-materials specialists had been deployed to O'Hare to await Padilla's arrival. But the landing at O'Hare International Airport at 1:30 p.m. was as uneventful as the plane ride. Once in the Jetway, Padilla was asked to accompany federal officials to the Customs and Immigration hall. Whisked away on a "material witness" warrant--which the Justice Department has repeatedly used to secretly detain suspicious foreigners and even U.S. citizens since September 11--Padilla was transported to the Metropolitan Correctional Center in Manhattan, the high-rise federal prison a few blocks from Ground Zero. No one outside of law enforcement seemed to notice the sudden disappearance of a stocky Hispanic man who was one of thousands arriving every day in America from overseas--not until a month later, when it was announced that Padilla had been moved to American military custody.

The story of Padilla's quiet capture is the best evidence yet that the war against Al Qaeda has entered an entirely new phase. If the war began dramatically, with planes crashing into buildings and the Taliban fleeing Afghanistan, it is now mostly underground--waged by terrorists, spooks, paramilitaries and G-men. It is, at last, the long twilight struggle George W. Bush promised, and then some; a shadow war that is equal parts Tom Clancy and John le Carre, with a little Torquemada thrown in, as U.S. allies like Pakistan and Egypt apply their own harsh interrogation techniques. The bounds of morality are unclear--and it may not be known until decades from now, when the histories are written, just how far America was willing to go to rid itself of this scourge. …