rom remote bases in Afghanistan's craggy mountains, a new breed of savage and suicidal terrorists built themselves an empire. Driven by a hatred for America and the West, they recruited thousands of angry young men and trained them for war. At makeshift camps of tents and caves, the self-styled Islamic warriors taught the tools of terror in between rigorous bouts of indoctrination into their fanatical warping of Islam. The disciples were then sent afar and told to disappear into the local culture until they could strike.

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Al Qaeda lorded over its Afghan haven with impunity, having essentially purchased the ruling hard-line (and bankrupt) Taliban government. They commandeered the nicest houses and seemed immune to Afghan law; many got away, sometimes literally, with murder. They developed an elaborate tracking system to keep tabs on their vast caches of AK-47s and explosives. Special stationery granted them free hotel rooms and other entitlements as they moved around the country. The most valuable operatives might be provided with (usually unwilling) Afghan wives or mistresses.

It was from this isolated land that al Qaeda took aim at the heart of America. The success of its brazen plot to turn airliners into missiles surprised even Osama bin Laden, the movement's Saudi exile leader, with its success. America's response was swift and uncompromising. It declared war. War on bin Laden, al Qaeda, its supporters, and terrorism writ large. But sophisticated weaponry and military might alone would never be enough. In just over a decade, al Qaeda cells had spread to as many as 60 countries. Its hierarchy remained opaque, and potential hideouts appeared infinite.

A war against such an elusive enemy, it was clear, would be an epic struggle. "Americans should not expect one battle," President Bush told Congress when he declared war on al Qaeda, "but a lengthy campaign, unlike any other we have ever seen." United in grief and outrage, the nation mobilized resources–military, intelligence, law enforcement, diplomatic, and financial–and harnessed moral outrage and fear.

The obvious starting point was al Qaeda's home in Afghanistan and its Taliban protectors. Simply destroying training camps, though, would not be enough. The United States would have to hunt down, and likely kill, al Qaeda's leaders. The problem was finding them. U.S. intelligence had been trying to track al Qaeda intensely for several years. "We had a window into Afghanistan," says a senior intelligence official. "We were going in and out." Despite a few promising leads on bin Laden's whereabouts, nothing worked.

This time, the Bush administration promised, it was going to be different. The Central Intelligence Agency would enlist a variety of Afghan opposition leaders and warlords to help, plying them with guns, money, and humanitarian goods ferried in on the CIA's own air fleet. After all, this was familiar territory for the CIA, which had supported the mostly Islamic struggle against the Soviet Union in the 1980s.

Sitting in the secret chambers of a Pentagon still smoldering from the September 11 attacks, the generals had to come to grips with an enemy unlike any they had been trained to fight. And with no preordained campaign plan for Afghanistan, war planners confronted an enemy with few valuable targets to destroy, an intelligence map with glaring holes, and a region with few strong U.S. allies.

Add to that an unforgiving terrain that had been a graveyard of empires throughout history. From the Victorian-era British legions to the Red Army, Afghanistan had punished the great armies of great nations, cutting the conquerors down to size with a brutal landscape and a patient people. A large-scale U.S invasion might have had similarly disastrous results, strengthening the hand of al Qaeda inside Afghanistan. The Bush administration also needed to make it clear that it was not conducting a "crusade" against Islam (a word Bush mistakenly uttered once). "[Bin Laden's] strategy is to make this into a war between the West and Islam," says a senior administration official. "This makes him the rallier of the Islamic cause."

So U.S. officials left the world's most powerful army at home and chose to fight the first war of the 21st century with a decidedly low-tech militia: the 15,000 men of the Northern Alliance opposition who had battled the Taliban to a stalemate over the past five years. With the aid of billion-dollar U.S. machinery striking targets from the air, the Northern Alliance would be used to overrun weakened Taliban positions and retake the country. It was a low-risk option, yet one with uncertain rewards. "It was a pickup game," says one Pentagon official. "We just kind of rolled with it to see what happened."

The war would rise or fall on the quality of the intelligence, and not everyone was sure that the CIA was up to the job. Were there any real spies left? When the Cold War ended, the CIA's Afghan contacts lapsed and its budget for covert operations atrophied. Yet back in 1997, the CIA had recognized the crippling decline of its Directorate of Operations and launched the "2005 Plan" to overhaul it. The aim was to rebuild everything–from language skills to paramilitary training–by 2005. Every DO recruit, for example, has since been required to undergo some special-operations training, such as jumping out of an airplane. The CIA had one other weapon–a network of retired spooks who knew Afghanistan and came back as contractors.

All this preparation meant that within days of September 11, CIA paramilitary teams were on the ground inside Afghanistan, meeting with opposition figures and scoping out potential targets. "After the 11th, the sanctuary was declared hostile territory, and that allowed a level of operation which we could still do clandestinely but which came with the full force of the U.S. military behind it," says a senior intelligence official.

As aircraft carriers steamed into the Arabian Sea, U.S. officials were securing access to 13 new bases from which to launch strikes into Afghanistan. Two special-operations task forces were created to conduct the war on the ground. Task Force Dagger was dispatched to a secret base in Uzbekistan to marry up with the Northern Alliance. Task Force K-BAR mounted its own commando operations.

The first bombs fell October 7. Twelve days later, Green Berets loaded up MH-47 Chinook helicopters in the black of night and flew over the Hindu Kush toward the rebel forces in northern Afghanistan. Earlier attempts to insert the Special Forces had been thwarted by bad weather and withering enemy ground fire, even though U.S. airstrikes had destroyed the Taliban's paltry air defenses. The first two teams went in that night, one to meet up with two Northern Alliance commanders–Abdul Rashid Dostum near the northern city of Mazar-e Sharif, and Muhammad Fahim Khan, north of Kabul. The ground war had begun.

It was America's first special-operations war, a war requiring a few tactics they had long ago stopped teaching at West Point. Sitting on horseback, Army and Air Force special-ops troops equipped with laser designators, laptop computers, and hand-held GPS devices called in deadly airstrikes in advance of cavalry charges against Soviet-era tanks. U.S. planes dropped not only precision-guided bombs but horse feed and Kalashnikov rifles. The results were dramatic. The Special Forces "turned the Northern Alliance into a conquering army," said Robert Andrews, who oversees special operations at the Pentagon.

When mapping out the strategy, the generals knew that taking Mazar-e Sharif would be essential to breaking the Taliban's grip on northern Afghanistan. If the Taliban lost that key city along the ancient Silk Road, its supply lines to the north would be cut off and the surrounding cities might fall in turn. With the north secure, rebel forces could then push south toward Kabul and Kandahar. Yet officials in Washington were not expecting a quick rout. As one defense official puts it, "We thought we would be lucky if we got Mazar to fall by Christmastime, and then worry about Kabul and Kandahar in the spring."

As it turned out, the dominoes fell much sooner. After a few tense weeks, the rebels quickly advanced through northern Afghanistan. Days later, on November 13, rebel forces rolled their aging tanks into Kabul. The strategy had paid off, easing the pressure on the U.S. Central Command in Tampa to insert a larger ground force into southern Afghanistan. "It became evident very quickly that the urgency for conventional forces wasn't there," says Commodore Robert Harward, commander of Task Force K-BAR. The Taliban body count was relatively low, and few prisoners were taken. Instead, the reckoning came in the traditional Afghan way: The defeated just switched sides.

In southern Afghanistan, Green Beret teams turned ethnic Pashtun tribes against the embattled Taliban regime and marched toward Kandahar. During the decisive battle of Tirin Kowt, in the heart of the pro-Taliban territory north of Kandahar, Pashtun fighters led by future prime minister Hamid Karzai defeated a numerically superior Taliban force with the aid of relentless U.S. air power. "When we took Tirin Kowt, it was like taking Richmond during the Civil War," says Capt. Jason Amerine, head of the special-forces team working with Karzai. "Hamid turned to me and said, 'We have broken the back of the Taliban.' "

Yet using Afghan fighters as a proxy force had its shortcomings. With the Taliban's grip on power dwindling, hundreds of al Qaeda fighters–perhaps even bin Laden himself–sought refuge in the mountain redoubt of Tora Bora, just miles from the Pakistani border. Central Command called on Afghan militia forces to search the cave complex while U.S. B-52 bombers pounded the fortress from above. Yet instead of killing or capturing the al Qaeda fighters, many of the U.S. "allies" cut deals and shepherded the enemy over the border into lawless tribal areas of Pakistan.

Top Pentagon officials continue to defend the tactics at Tora Bora, saying that it would have taken U.S. marines in southern Afghanistan as much as three weeks to train for the mission. Yet many in the military see Tora Bora as the one glaring failure of an otherwise successful Afghan campaign, a lost opportunity born out of a fear of excessive U.S. casualties. In the words of a senior special-operations officer, "It was a waste of time because we weren't allowed to do it unilaterally."

The war widened as al Qaeda fled across the border into Pakistan. In many ways, the Afghan campaign had been the easy part. Washington now faced an even more amorphous target–the thousands of al Qaeda-trained militants spread throughout Asia, the Middle East, Europe, and North America.

The news wasn't all bad. Al Qaeda was clearly reeling. Its feared military chief and the operational mastermind be- hind 9/11, Mohammed Atef, was killed in a U.S. airstrike. Worldwide, authorities had bagged a good number of al Qaeda's midlevel operatives.

But by August 2002, only one third of al Qaeda's top 30 leaders were believed dead or captured. "Al Qaeda is a global, multiheaded hydra," says terrorism expert Magnus Ranstorp. "If you cut off one head, it grows another." Some leaders are believed to be regrouping in hide-outs throughout Pakistan's remote tribal areas and its cities, and also in Yemen and Saudi Arabia. U.S. intelligence agencies have intercepted communications suggesting that these remnants are plotting new attacks.

The military had, in effect, bombed itself out of a job. "We wanted to deny the terrorists their base of operations," says a top military officer. "What happened in the process is that we lost our primary target of al Qaeda." With the Karzai regime in power in Kabul, the military focus turned to a manhunt through crowded cities and tiny villages perched in Afghanistan's eastern mountains, and, occasionally, across the border in Pakistan. U.S. and coalition commandos came across weapons caches and al Qaeda documents, some of which are paying dividends in U.S. courtrooms. (In one safe house, Special Forces found documents that seem to link alleged shoe bomber Richard Reid to al Qaeda.) Seven thousand U.S. troops remain in Afghanistan, helping to protect a fragile government from regional warlords. Elsewhere, Special Forces have fanned out to the Philippines, Yemen, and Georgia to train and equip local troops for the war against terrorism, and covert special-operations units are planning raids to nab bin Laden's closest henchmen. "You have to go after the Richard Reids, and we'll do that," the chairman of the Joint Chiefs, Gen. Richard Myers, tells U.S. News. "But there are others that are probably more important in the planning and financing process, and they would be the ones most interesting to us."

This is where the intelligence agencies come in. The CIA doubled the size of its Counterterrorism Center to more than 1,000 analysts and case officers. "This in an offensive game, not a defensive one," says Jack Devine, who ran the CIA's covert side in the mid-'90s. "We need to go on the offensive before they get on a plane to come here." CIA officers have been deployed around the world, as the agency tries to shake off the risk-averse, scandal-fearing culture that plagued the CIA in the 1990s. "Today, the year 2002, I have more spies stealing more secrets than at any time in the history of the CIA," Deputy Director for Operations Jim Pavitt said recently. But al Qaeda is perhaps the most challenging target ever for the CIA. Traditional measures simply don't work. "Do I, in a pinstriped suit, have the ability to sit comfortably, camp-side in Afghanistan and talk to a terrorist who is planning an attack against the embassy in Islamabad?" asks a senior intelligence official. "I need a surrogate."

Currently, U.S. intelligence is relying heavily on its foreign counterparts. President Bush tried to leave countries with little choice in the matter. "Either you are with us, or you are with the terrorists," he said on September 20. In all, some 90 countries have detained more than 2,400 people with alleged terrorist ties. Countries like Jordan and Pakistan have risked a serious backlash from their own Islamic militants to pursue al Qaeda suspects. In one high-profile operation conducted by CIA, FBI, and Pakistani authorities, al Qaeda's chief of operations, Abu Zubaydah, was arrested and handed over to the U.S. military. His interrogations, while likely sprinkled with disinformation, have been a treasure-trove of details about al Qaeda. Even traditional adversaries like Syria and Iran cooperated in aspects of the war on al Qaeda. Syria, for instance, agreed to detain and interrogate a senior al Qaeda leader, even passing information back to Washington.

The most important victories have been overseas, where al Qaeda cells have been rolled up in places like Spain, France, Morocco, and Singapore, preventing planned attacks. Still, in most of these cases, Washington is playing only a supporting role. "It doesn't depend on [U.S.] intelligence as much as it does on the local authorities in those countries," says Vincent Cannistraro, who once ran the CIA's Counterterrorism Center.

In Singapore, for example, police busted an al Qaeda cell that was plotting against the U.S. Embassy and U.S. military targets. The first tip came to police last September when a local told them about an Islamic extremist claiming to know bin Laden. In December, after further investigation, Singaporean police arrested a number of suspected al Qaeda militants. A few days later, the U.S. military briefed Singaporean officials about a videotape found in Afghanistan that showed surveillance of targets in Singapore. The cell turned out to be part of a larger network with cells in Malaysia and Indonesia.

At home, law enforcement agencies were given unprecedented powers to use more intrusive measures to investigate terrorism suspects and detain them, secretly if necessary. A man accused of plotting to detonate a radiological bomb was declared an "enemy combatant" and shipped to a U.S. base in South Carolina; most of the al Qaeda prisoners from Afghanistan have been sent to an American base at Guantánamo Bay, Cuba. The FBI is remaking itself, with preventing terrorist attacks its top mission. All told, the FBI deployed 4,000 agents to trace the 9/11 plot, its largest investigation ever. But it's not easy for an agency used to fighting mobsters and drug lords. After 9/11, agents rounded up hundreds of suspects who were held secretly on suspicion of terrorism. Most had no terrorism charges filed against them and were simply deported.

The terrorism war is governmentwide. The Treasury Department began tracking terrorist financing, freezing some $34 million in alleged terrorist assets. Other domestic agencies ranging from the Immigration and Naturalization Service to the Coast Guard went on heightened alert. The real fear is that sleeper cells remain in place, posing a danger at home and abroad. "A lot of determined people are still ready to do us harm," warns Republican Sen. Richard Shelby, vice chair of the Senate Intelligence Committee.

But the finite limits of the government's ability are becoming clear as well. The U.S. military cannot operate freely in al Qaeda hideouts like Pakistan. Many of the hardened terrorists have not cracked under interrogation. Terrorists are finding new ways to communicate that are more difficult for the National Security Agency to intercept, and al Qaeda's financing is still flowing. "There are still massive amounts being transferred out of Saudi Arabia," says terrorist expert Ranstorp. U.S. foreign policy is also threatening to cleave the diverse international coalition fighting terrorism. Key Arab countries in particular, already resentful of U.S. support for Israel, might abandon the war if the Bush administration follows through on threats to attack Iraq.

Optimists take heart that there has not yet been another serious al Qaeda attack since 9/11. Should al Qaeda manage to pull one off, though, U.S. options will be limited. There are no other Afghanistans out there. "If there was a terrorist strike in the future, who do we strike back at and where do we retaliate?" asks Devine. Perhaps a bigger problem is that nobody knows when, or if, the war will ever end. "You never win the war on terrorism," warns John Gannon, a former CIA deputy director for intelligence. "You only reduce the threat."