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.

“We must take the battle to the enemy, disrupt his plans and confront the worst threats before they emerge,” Bush told West Point graduates a few weeks ago. Many commentators thought he was talking about pre-emptively striking future foes like Iraq. But Bush was also putting a new emphasis on covert operations, which has raised fresh concerns about civil liberties. How far is America veering toward police-state tactics? “We shouldn’t deceive ourselves. This is not a defensive game,” says Jack Devine, a former CIA associate deputy operations director. “If we seal our ports, they’re going to come across the Rio Grande, or from Canada. The truth is that [with new homeland security] we’ll improve defensively by maybe 7 percent or 10 percent. The best hope we have is to go after and destroy the terrorist organization.”

U.S. intelligence has no clear picture of how Padilla was recruited to Al Qaeda (story, page 34), or how many other American converts might have joined him. But as the Taliban collapsed last year and the U.S. air campaign blasted one of Al Qaeda’s last strongholds at Tora Bora, Abu Zubaydah fled across the rugged mountains, and Padilla traveled with him, along with hundreds of other terrorists, Pakistani investigators believe. Zubaydah, a thirtysomething Palestinian in charge of Al Qaeda’s network of terrorist-training camps, had decided to reconstitute deep inside Pakistani cities with the assistance of Pakistani extremists.

Their retreat stopped for a time in Peshawar, the biggest city along the Afghan frontier. But Arabs like Zubaydah and foreigners like Padilla stood out too starkly among the ethnic Pashtuns along the border. So they and their Pakistani sponsors decided to move Zubaydah and his men to Pakistan’s second largest city, Lahore, 250 miles to the southeast. Al Qaeda had several safe houses, equipped with satellite phones and laptops with Internet connections, up and running by late January. Pakistani investigators say Padilla spent most of February in Lahore surfing the Net in search of how to make a radioactive bomb.

For his part, Abu Zubaydah moved again, this time to the grimy industrial town of Faisalabad. He lived there with other Qaeda and Pakistani militants in a nondescript two-story house surrounded by a high wall, on top of which they installed a fence of high-voltage electrical wires. From there, Abu Zubaydah presided over the expansion of Qaeda cells in other large Pakistani cities, especially Karachi, a multiethnic, coastal metropolis of 12 million, where foreign Qaeda can blend in.

Padilla first surfaced in February when he went to the American Consulate in Karachi to get a new passport. The consulate, suspicious of a Hispanic with an assumed Muslim name in Pakistan, later flagged U.S. intelligence operatives, including FBI investigators. Not long afterward, American officials say, Pakistani authorities detained Padilla and a non-American associate for investigation on possible immigration violations, then let them go.

Around the same time, CIA technicians were homing in on Zubaydah’s many satphone calls from Faisalabad. On March 28, local authorities, assisted by FBI and CIA representatives, conducted raids on about a dozen suspected Qaeda safe houses around Pakistan, capturing huge caches of Qaeda computers and documents. More important, they seized a number of suspected Qaeda operatives, including Zubaydah. Gravely wounded in a shoot-out, Zubaydah began to tell interrogators about how he had hooked up late last year in the Afghan city of Khowst with an American-born Qaeda recruit whose name he didn’t know. As the two men escaped Afghanistan together, Zubaydah said, the American would-be terrorist told him he had a big plan to launch a major attack on his homeland. The plan involved creating and detonating a radiological dispersion device, contaminating a wide area and creating huge economic disruption. Since he was not an expert in dirty-bomb construction, Abu Zubaydah told his interrogators, he arranged for the U.S. recruit to meet with Qaeda operatives inside Pakistan who had such expertise.

While Zubaydah was spinning this tale, U.S. intelligence operatives pored over physical evidence seized from his safe house and other raided Qaeda locations. Documents, possibly including a photocopy of Padilla’s passport or identity papers, appeared to confirm Zubaydah’s story. Other evidence, including images recovered from seized Qaeda computers, indicated the American recruit had been gathering information on dirty-bomb construction.

By late April, the pieces of the puzzle were coming together: U.S. intelligence agencies had linked the suspicious Hispanic in Karachi with Zubaydah’s description. Other Qaeda prisoners, possibly including detainees sent to the U.S. prison in Guantanamo Bay, Cuba, gave interrogators information that seemed to confirm Padilla’s identity. Eventually, investigators reportedly took passport photos of Padilla and his suspected accomplice to Zubaydah at his secret prison. Were these the dirty-bomb suspects that he was talking about? They were, Zubaydah told his interrogators.

On April 24, less than a month after the capture of Zubaydah, U.S. officials told NEWSWEEK, the name of Jose Padilla was placed on the secret “watch list” of terrorism suspects. American intelligence now knew who Padilla was, and what his plan was. But they no longer knew where he was because he had already flown out of Karachi and was on his way to a mysterious visit to Cairo by the time Zubaydah began to sing. In late April, anxious analysts began to comb through international travel records. Two weeks after Padilla’s name and alias were placed on the border watch list, a U.S. intelligence analyst got lucky. Studying air-travel records, the analyst came upon a garbled version of the name Jose Padilla, with a reservation to travel on Swiss International Air Lines on May 8.

One question is why Zubaydah, a fanatical anti-American, told investigators anything at all. Such is the nature of the shadow war that little is known about what goes on inside the interrogation rooms. U.S. officials insist they aren’t sanctioning torture, but physical discomfort like sleep deprivation, sustained with bright lights and marathon questioning, can work. “I would hope they’re using it,” says an ex-FBI senior counterterrorism official. And if that doesn’t work? “Some of the real bad asses, they’ve been flying them back to their home countries: Jordan, Egypt, Saudi,” where questioning can involve beating and worse, says one well-informed Arab source.

Zubaydah himself may be in such a place. His whereabouts are a national-security secret kept almost as zealously as the Manhattan Project; even CIA officials who are briefed on his interrogation don’t know where he is being held overseas. Some U.S. officials believe Zubaydah is playing them, perhaps tossing overboard amateurish small fry like Padilla to preserve “the crown jewels,” as one CIA official calls whatever key plotters may be left. But U.S. authorities and their allies are playing with Al Qaeda as well. They have publicly attributed many recent threats to Abu Zubaydah, perhaps as a way of demoralizing Al Qaeda, getting his confederates to talk or signaling that every operation the terrorists have planned may be compromised. And his own people are talking, among them his deputy, Ibn Al-Shaykh al-Libi, who was captured by Pakistani forces in late December or early January and quickly turned over to U.S. interrogators. By the end of January, al-Libi had disclosed enough to disrupt an alleged Qaeda plot to attack the U.S. Embassy in Yemen, a longtime Qaeda hotbed. U.S. officials acknowledge that information from al-Libi also played a part in the capture of Abu Zubaydah himself.

While Al Qaeda lies low, it seems that U.S. authorities have been stashing key suspects around the globe. Mohamed Haydar Zammar, a Syrian-born German believed to have been part of Mohamed Atta’s 9-11 cell in Hamburg, is an example. Tailing him last fall, German investigators at first had trouble finding sufficient evidence to justify an arrest under their strict evidentiary requirements. So they issued him a temporary passport and let him travel to Morocco. There Zammar just disappeared, and his family later filed a missing-persons report. A U.S. intelligence official confirms he is in custody overseas, but would not say where. The Germans, supposedly stalwart U.S. allies, say Washington hasn’t told them.

Similarly, the bush adminstration says it put Padilla into military detention when it concluded that the sources and methods used to capture him were too sensitive to reveal in open court. But the decision also came shortly before his court-appointed U.S. lawyer was preparing to challenge his arrest in court. If the courts had agreed to hear the case, Padilla would have had to be granted regular access to a lawyer and some modicum of rights. As an illegal combatant in the custody of the military, however, he can be held indefinitely, and interrogators, for the moment, won’t have to worry about lawyers’ and judges’ looking over their shoulders. U.S. officials also want to avoid the soapbox nature of Zacarias Moussaoui’s trial in Washington, which gives terrorists an opportunity to promulgate their world view publicly.

What was Padilla’s real plan, and how far along was it? Perhaps the endless interrogation he is now undergoing will tell. What American officials at O’Hare didn’t do–but were tempted to–was to tail Padilla once he landed to see whom he was meeting. Jittery after a torrent of criticism over other lost suspects–principally the hijackers of September 11–the FBI decided he was too dangerous to take a chance with. As a result, U.S. officials say, they simply do not know whether Padilla was a lone wolf, or had a network of confederates in America. And if there is a nationwide manhunt for any accomplices, that, too, is taking place off the radar. All of which points up the main problem with conducting a secret war: it’s difficult to tell who’s winning.

Sometimes not even the Feds know what the tally is–which doesn’t bode well for the new spirit of intel cooperation in Washington. Just before Padilla’s flight, some American intelligence officials back in Washington became alarmed when they noticed that an abnormally large number of Swiss and U.S. passengers had booked last-minute passage on the same plane: it took a while for word to get through to the analysts that the last-minute passengers were the Swiss and FBI teams tailing the suspect. Even the White House, Pentagon and Justice Department couldn’t seem to agree on what kind of threat Padilla posed. When Attorney General John Ashcroft announced portentously that Padilla was plotting a radiological bomb attack, White House officials scoffed privately; Deputy Defense Secretary Paul Wolfowitz countered that the “plot” was mostly still talk.

There are other worrisome signs that terror could prove more slippery even than U.S. tactics to contain it. Late last week FBI agents were running down a warning from Canadian intelligence that Qaeda operatives might be targeting the G8 summit in Canada later this month. Last Friday, two months after Padilla showed up at the U.S. Consulate in Karachi, the fortified building’s guardhouse was struck by a car bomb that killed at least 11 people (no Americans). The attack was strikingly similar to a suspected Qaeda strike on a Pakistani naval bus in May, which slaughtered 14 people, including 11 French naval technicians. The surviving suspects slipped away. Despite a crackdown in Pakistan, its cities remain hosts and seedbeds for radicals. And while terrorists no longer have a haven in Afghanistan, they’re now forming what one intelligence official calls “virtual training camps” on the Web. For the last two months, individuals in a U.S.-based Internet chat room have been frantically conversing, clearly wanting and planning to attack the United States, law-enforcement authorities say. At least one chat-room participant was asked if he could speak Spanish, since terrorist recruiters are looking for Arabs or other Muslims who “look Latin” and speak Spanish “to infiltrate the U.S.” All we can be sure of today is that they have one fewer recruit in Jose Padilla.