Wherever he was hiding, bin Laden must have been contemplating his own doom. His Afghan benefactor, Taliban leader Mullah Mohammed Omar, relinquished control of the extremists’ stronghold at Kandahar last week, even as U.S. forces continued to relentlessly bomb the mountain hideouts of Qaeda and Taliban forces. According to British intelligence, the bombs may have hit bin Laden’s closest lieutenant, Egyptian doctor Ayman Al-Zawahiri, whom many consider the brains behind Al Qaeda. (The reports, based on communications intercepts, could not be confirmed by U.S. intelligence; family members in Cairo published a newspaper notice saying that Al-Zawahiri’s wife and children had been killed.) An American guided bomb had already taken out bin Laden’s top military commander, Muhammad Atef, four weeks earlier.

Now some of bin Laden’s soldiers, fiercely defending Tora Bora caves against attacks by anti-Taliban Pashtun fighters, were desperate. Using megaphones, they shouted in Arabic down the ravines: “We’re Muslims and you’re Muslims. Muslims shouldn’t fight each other!” But it was a little late for appeals to Muslim brotherhood from militants who had been trying to exterminate their Afghan enemies for years.

Bin Laden and Mullah Omar must be wondering what has become of their grand designs to remake the world. Both men believed that Afghanistan would be the first building block in an Islamic-militant empire that would stretch, eventually, across the planet. Omar, a half-educated, one-eyed warrior with almost no knowledge of the wider world, regarded himself as the commander of the Muslim faithful, a title that no leader had claimed in centuries. And the savvy bin Laden had stoked Omar’s megalomania, in large part because he needed Afghanistan as a base to achieve his own ambitions: to wage an epochal war against the infidel West. Bin Laden called his organization Al Qaeda–the Base–because he saw it as a headquarters’ operation for a much wider and diffuse movement. But the real “base” was Afghanistan, a country honeycombed with Qaeda safehouses, training camps and mysterious research facilities. And now, for all practical purposes, Afghanistan has fallen to bin Laden’s foes.

A wealth of new information from inside Afghanistan reveals the extent to which bin Laden’s foreign forces had “colonized” the country–and the magnitude of what it meant to Al Qaeda’s operations. Yet the campaign to hit Al Qaeda outside of Afghanistan has not been nearly as successful as the military campaign to destroy the leadership. A complex network of Qaeda operatives remains at large, including U.S.-based cells. One of those cells, NEWSWEEK has learned, nearly launched an attack on a major target in Washington, D.C., after September 11.

Intelligence sources told NEWSWEEK that a Qaeda “sleeper cell” in the United States was poised to launch the attack–perhaps against the Capitol Building–not long after the 9-11 atrocities. The sources believe that the FBI, in its sweep against visa violators and other suspects of Mideast backgrounds, picked up members of a “support cell” tasked with providing logistics help to the people actually carrying out the mission. The would-be terrorists then went underground or fled the country, intelligence sources say. Yet it is not clear whether investigators have been able to identify the plotters from among the hundreds of people caught in the FBI dragnet.

Finding the terrorists who are still operating at home and abroad may be the No. 1 problem now, even as bin Laden’s world falls down around him in Afghanistan. The war has produced a hodgepodge of disturbing intelligence that investigators are still trying to sift and analyze. Perhaps the most alarming evidence gathered so far concerns Al Qaeda efforts to develop biological weapons. According to intelligence sources, U.S. operatives in Afghanistan have collected information that one or more Russian scientists were working inside Afghanistan with Qaeda operatives. One well-placed source told NEWSWEEK that evidence from the scene indicates that the renegade Russians were helping Al Qaeda to develop anthrax, and that spores of the deadly disease may actually have been stockpiled by the terrorist group. While the source believes any such stockpiles were destroyed in U.S. bombing raids, it is not known how much, if any, of the anthrax ever made it out of Afghanistan.

The infamous Dr. Al-Zawahiri may have been directly involved in the biological program. A senior American intelligence official told NEWSWEEK that Al-Zawahiri’s house in Kabul resembled the lair of a mad scientist. Northern Alliance soldiers who raided the house on Nov. 13 found grenades, blasting caps, electronic components and “various solid and liquid substances.” These included white crystals and extremely fine, silvery powders in jars and plastic bags, and mysterious liquids in shampoo bottles labeled special medicine. American intelligence later collected samples from Northern Alliance colleagues and conducted chemical and biological tests. One of the samples turned up a “positive indicator” for Bacillus anthracis, or anthrax. All of the samples are being retested, the source told NEWSWEEK.

The Kabul house of a Pakistani nuclear scientist, Sultan Bashiruddin Mahmood, contained sheaves of disturbing documents. These include the results of a massive Internet search on anthrax vaccines, and a report titled “Bacteria: What You Need to Know.” According to intelligence sources, investigators also found a report titled “Iraqi Anthrax Troops,” and a New York Times article on Plum Island, the U.S. Department of Agriculture’s animal-disease center near the north fork of Long Island. The Plum Island center does research to help guard the United States “against catastrophic economic losses caused by foreign animal disease agents accidentally or deliberately introduced into the U.S.,” its Web site explains.

The intelligence revelations raise troubling questions. Following the fall of Kandahar, and the formation of a U.N.-backed interim administration to rule Afghanistan starting Dec. 22, one question remains paramount: can the global Qaeda network thrive without Afghanistan as a base, and without its key leadership? On the good-news front, Al Qaeda’s training-and-logistics organization in Afghanistan appears to have been more central to the group’s development and cohesion than many analysts had thought. Most evidence suggests that major attacks on U.S. targets in recent years–the bombings of African embassies in 1998 and the destroyer USS Cole in 2000–were largely coordinated and organized from inside Afghanistan. On the other hand, intelligence gathered to date suggests that the worst attack of them all, on September 11, was substantially planned in or supported from places outside of Afghanistan. It appears to have had its origins in the cell in Hamburg, where lead hijacker Mohamed Atta lived for eight years. And it seems to have been developed in contacts with other European cells, and received funding through Dubai.

Questions about the nature of the organization itself remain unanswered, too. Al Qaeda is widely likened to a cult, and some believe that it will wither and die once its charismatic leaders are gone. Others argue that it could mutate, like a disease, into something potentially more furtive–covert cells that have no public “face” or base to strike back at. Still, if Al Qaeda lives on in that form, such disaffiliated cells may be less capable of launching a coordinated, sophisticated attack like that of September 11. And they’ll be operating in a much more vigilant environment. Since September 11, antiterror laws have been strengthened in some countries, financial networks have been hindered and intelligence cooperation has intensified.

What investigators do know today, three months after the attacks on New York and Washington, is this: it took the fertile soil of fundamentalist Afghanistan to grow Al Qaeda from a relatively small outfit to a thriving global organization. Analysts now realize there was almost no difference between Al Qaeda and “foreign” Taliban forces; the terrorism impresario had all but hijacked the country and its hapless leader Mullah Omar, and had free run of it. Investigators know that Al Qaeda had roughly 40 training camps throughout Afghanistan. German federal police investigating Al Qaeda’s Hamburg cell, whose members included three of the September 11 hijackers, believe that as many as 70,000 Muslims from dozens of countries passed through the camps over a period of several years. (That figure far surpasses estimates by the CIA, which puts the number at 15,000 to 20,000.) Some of the Arab and other foreign graduates of the camps fought in front-line Taliban units. Others attended more specialized camps that focused on bomb-making, sabotage and use of chemical weapons.

The Afghan base provided Al Qaeda with many of the advantages of a state infrastructure. Officials at the Ministry of the Interior’s “public-identity office,” for instance, say they issued about 15,000 Afghan identity cards to foreign militants during the past three years. Al Qaeda offices in Kabul have yielded stacks of Afghan passports, as well as forged documents from Pakistan and many other countries.

Bin Laden plied his Taliban hosts with money, gifts and other favors. “He was always handing out $50,000 to this commander, or $10,000 to that commander,” says Mullah Alhaj Khaksar, a senior Taliban defector. “And cars–Afghans love cars. He would get 20 or 30 cars and bring them in from Kandahar as a present just before an offensive.” Western intelligence agencies estimate that bin Laden funneled as much as $100 million a year to the Taliban–twice Afghanistan’s official annual budget.

That staggering amount doesn’t surprise the chief pilot of Ariana Afghan Airlines, Said Nabi Hashimi. By 1998 Ariana could no longer fly to most destinations in the world. But before U.N. sanctions were imposed in late 2000, the Taliban and Al Qaeda kept the airline’s planes busy shuttling to Sharjah and Dubai in the United Arab Emirates. Mysterious passengers often boarded the planes in Kabul using Ariana crew IDs. “They would be people we had never seen in our lives,” says Hashimi. And when the pilot asked his Taliban-appointed bosses about the strange “employees,” he was told they were friends of ministers or other VIPs. In Dubai, the men were able to disembark without passing through standard customs or immigration controls.

More mysterious was the appearance in mid-1998 of an airstrip deep in the Rigestan Desert, about 150 miles southwest of Kandahar. At night “it looked like a small city down there,” Hashimi said. “There were so many lights.” There were even runway lights–“they could land aircraft of any size in there, day or night.” When the controllers at Kandahar asked an incoming flight’s destination, the aircrafts’ pilots would respond “the Strip,” in English, and nothing more. “We could tell they were big planes… because they were coming in from [28,000 or 31,000 feet], and only a big, pressurized plane flies that high. At one point there were as many as six or seven big planes coming in every day, night and day.” It seems clear now that the Taliban and Al Qaeda were running a large logistical operation, moving men, weapons and other supplies.

Al Qaeda will no longer be able to use Afghanistan as a kind of organized breeding ground for militants. But Afghans never really became part of bin Laden’s international organization anyway, and tens of thousands of foreign extremists have already learned military and terror skills and moved on. Hundreds if not thousands of hard-core militants are still at large, including many who were involved in previous terrorist operations. They know how to raise their own money, even if Al Qaeda’s funds are blocked, and they have knowledge that can be passed on to other extremists.

Some key fugitives appear to have had a hand in both the bombing of the USS Cole in Yemen and the September 11 attacks. Investigators are particularly interested in a meeting that took place in Malaysia on Jan. 5, 2000. The list of attendees included Tawfiq bin Atash (a.k.a. Khallad) and Fahad al-Quso, both of whom helped plan the Cole attack. Also present were Khalid Almihdhar and Nawaf Alhazmi, two of the September 11 hijackers, and Ramzi Binalshibh (a.k.a. Ramzi Omar), who may have been the phantom “20th hijacker” who couldn’t get into the United States prior to September 11 because of visa problems. NEWSWEEK has learned that when Almihdhar and Alhazmi left Malaysia, they flew directly to Los Angeles, where they quickly enrolled in a San Diego flight school. That leads investigators to believe that at least some of the planning for September 11 took place at the Malaysia meeting.

The hijackers are now dead, of course. But what about their colleagues and presumed handlers? The United States has no idea of the whereabouts of bin Atash, who once commanded bin Laden’s bodyguards and who served as operational chief of the Cole bombing. Binalshibh traveled to Spain in the summer of 2001, at the same time hijacker Mohamed Atta was there. And on Sept. 5, the FBI believes, he flew to the United Arab Emirates, the financial hub of the September 11 operation. He disappeared on the 10th and hasn’t been seen since.

Western governments have arrested perhaps a couple dozen of known Qaeda suspects since September 11. The post-September 11 dragnet by American law-en-forcement agencies has caught roughly 100 people who were subsequently charged with crimes by federal prosecutors; another 550 or so are being held for violating immigration laws. None of those charged has been directly accused of involvement in the September 11 attacks, however. Only a few have been accused of abetting the 9-11 terrorists (by providing fake IDs, for instance), or lying about their contacts with the hijackers.

In the most optimistic reading of the current situation, America has delivered such a blow to Al Qaeda that even hard-core elements will realize the struggle is over now. But that almost certainly underestimates the zealotry of bin Laden’s followers, or their capacity for martyrdom.

Few militants could have been in worse straits last week than an Egyptian fighter named Abu Talha Rashid, who lay wan and wounded in the filthy, soot-coated backroom of an Afghan villager’s hut near Tora Bora. Educated at the prestigious American University in Beirut, Rashid and his brother came to Afghanistan in 1998. But now Rashid didn’t know whether his brother–last seen in Konduz–was dead or alive. And Rashid’s right leg was severely fractured (from a tumble down a steep mountainside), badly swollen and intensely painful.

Yet despite his dire condition–or perhaps because of it–Rashid still burned with anti-American hatred. “Maybe the Taliban loses all of Afghanistan, but it doesn’t mean Islam loses,” he said. “The history of Islam will never forget how Mullah Omar sacrificed his government for Islam.” Rashid couldn’t move his toes, but still expected that God would give him health–or usher him to the afterlife. “When I hear the sound of American aircraft,” he told a NEWSWEEK reporter, “I pray for death at American hands.” That’s one Qaeda prayer, at least, that may be answered to Washington’s satisfaction.