Five weeks ago, John Walker Lindh, better known as the American Taliban, was quietly transferred to a medium-security prison northeast of Los Angeles, in the Mojave Desert. He was relieved by the move, which took place after federal officials in Alexandria, Virginia, had debriefed him for a year about his knowledge of Muslim extremists. His temporary cell in Virginia had reminded Lindh of a dog kennel; his meals were delivered through a metal slot in the door, and he had no interaction with other inmates. At the new prison, Lindh has a roommate and a window. On occasion, he can mingle with the general prison population, which includes about twenty other Muslims, most of them American-born converts like himself. His main diversions are translating ancient Arabic religious texts and reading. His lawyers recently bought him a subscription to the New York Times, and now that he’s back in California, where he was raised, he has asked to receive the Los Angeles Times. Lindh has also met his goal of reading a hundred books during his first year in prison. His favorites have included Dostoyevsky’s “The Brothers Karamazov,” Viktor Frankl’s “Man’s Search for Meaning,” and the Harry Potter novels, whose publication passed him by while he was cloistered in the Islamic madrasahs of Pakistan and camped alongside Taliban soldiers in Afghanistan.

In the Lindh case, the prosecutorial zeal of the Ashcroft Doctrine appears to have weakened the government’s position. Illustration by Steve Brodner

Lindh, who is now twenty-two years old, pleaded guilty last summer to having aided the Taliban regime. He is due to spend the next twenty years in prison. Ordinarily, a first-time offender convicted of a single, nonviolent felony would be spared such a long sentence. Lindh, however, is the first American to have been successfully prosecuted as part of the Bush Administration’s war on terrorism. Lindh was accused not only of embracing the beliefs of people who hated his own country but also of taking up arms with them and being connected to the death of a young C.I.A. officer, Johnny Micheal Spann. From the moment Lindh was captured, in December of 2001, he was widely condemned as a murderous traitor.

The Justice Department, in particular, promoted this view. Before Lindh was indicted, Attorney General John Ashcroft held a press conference in which he revealed that the department planned to charge Lindh with “conspiracy to kill nationals of the United States” and with “providing material support” to Al Qaeda. Ashcroft declared that Lindh’s “allegiance to those fanatics and terrorists never faltered, not even with the knowledge that they had murdered thousands of his countrymen.” When Ashcroft announced the indictment, which included ten counts, he described Lindh as “an Al Qaeda-trained terrorist.” Lindh faced the possibility of three life sentences plus an additional ninety years in prison.

This past summer, however, the government abruptly dropped nine of the original charges. The case was settled in a weekend-long flurry of negotiations that ended at 2 a.m. on the day that key evidence against Lindh was to be challenged in open court. As part of the plea agreement, Lindh accepted guilt on a charge that was not directly related to terrorism: violation of a 1999 executive order forbidding American citizens from contributing “services” to the Taliban. Ashcroft’s high-profile prosecution effort mysteriously imploded. The Attorney General was not entirely convincing when he declared that Lindh’s plea agreement was “an important victory in the war on terrorism.”

Today, the government continues to regard Lindh as an enemy of the state who poses a serious danger to national security. Lindh is therefore covered by Special Administrative Measures, which prohibit him from speaking to the media. Bryan Sierra, a Justice Department spokesman, declined “to discuss the legal basis” for this decision, but noted that “such measures are intended to monitor activity in the most dangerous cases, to prevent them from plotting violent acts.”

With this gag order in effect, and with many documents in the case still classified, much remains unknown about why the prosecution collapsed. Fragments of this story, however, have lately begun to emerge. Lindh’s own words have surfaced in the form of notes taken during lengthy conversations with him by people involved in preparing his defense. In addition, a former Justice Department lawyer who is troubled by the government’s handling of the case has decided to speak out.

Rohan Gunaratna, a respected terrorism scholar from Sri Lanka, interviewed Lindh for more than eight hours last summer in Alexandria. Gunaratna, who is affiliated with the University of St. Andrews, in Scotland, is the author of six books, including the recent “Inside Al Qaeda.” A short, compactly built man with a friendly, wide face, Gunaratna met with me recently in Manhattan. He said that he had been wary when Lindh’s defense lawyers first approached him about serving as an expert witness. He warned them that he believed that Lindh was almost certainly a member of Al Qaeda. The defense, undeterred, pressed him to meet the young suspect, and Gunaratna eventually agreed.

The encounter surprised him. “I have interviewed maybe two hundred terrorists over the past few years,” he told me, “and I am certain that John Walker Lindh has never been a terrorist, and never intended to be one.” Peering over his round spectacles for emphasis, he said, “A terrorist is a person who conducts attacks against civilian targets. John Walker Lindh never did that. He trained to fight in the Afghan Army, against other soldiers. He was not a member of Al Qaeda. He didn’t know much about Al Qaeda, and he was no exception. Dozens of others whom I’ve met who went to train and fight in Afghanistan also were not part of Al Qaeda.” He laughed. “It’s a secret organization.” Gunaratna believes that Lindh “presents no national-security threat. He’s been completely misrepresented to the American people.”

Gunaratna’s talks with Lindh started with standard gambits to create trust and rapport. They discussed Lindh’s health and his treatment in prison. Soon, however, Gunaratna moved on to a close examination of what Lindh was thinking when his life first tilted toward radicalism, in the fall of 2000. Lindh, who converted to Islam during high school, skipped college in favor of studying Arabic in Yemen. With his parents’ approval, he abandoned this instruction in favor of a fundamentalist education at a madrasah in Bannu, Pakistan. He spent his days memorizing the Koran.

By the spring of 2001, Lindh told Gunaratna, he had become convinced that a proper Muslim needed to do more than read and pray. “I believed it was the part of every good Muslim to train” for military jihad, he said. His hope, he said, was to help create a “pure Islamic state.” Leaving his studies, he joined an Islamic paramilitary program run by Harakat-ul-Mujahideen (H.U.M.), a Pakistani organization that trained Muslims to fight against Indian security forces in Kashmir. The group’s guerrilla war against India enjoyed widespread popular support in Pakistan.

Some of its members, Gunaratna knew, had participated in kidnappings and suicide bombings. A schismatic offshoot of H.U.M. is thought to be responsible for the murder, last winter, of the Wall Street Journal reporter Daniel Pearl. The indictment states that Lindh “did knowingly conspire” with a “terrorist group dedicated to an extremist view of Islam.” Lindh told Gunaratna, however, that he had been “unaware” that H.U.M. was a terrorist organization.

Tamara Sonn, an expert on Islam who teaches at the College of William and Mary, also examined Lindh for the defense. She heard a similar story from Lindh. He told Sonn that he had hoped to enlist in the Kashmir fight to help “poor Muslims being oppressed.” His understanding of the complex conflict between Pakistan and India, Sonn said, was not sophisticated. “He’s not someone who is politically aware,” she told me. Although Sonn found Lindh to be “intelligent,” he also seemed callow. His knowledge of Islam struck her as “idiosyncratic” and narrow. He had memorized the entire Koran, she noted, yet he was not worldly about contemporary Islam. For example, Lindh expressed blank surprise when Sonn mentioned the Taliban’s condemnation of Shiites and the regime’s medieval constraints on women. “I’d have to study that,” he told her, saying he didn’t know much about it.

“I wondered, How could he not know?” Sonn said. ‘‘He was mystical, almost.’’

Lindh’s romanticized vision of jihad was hardly matched by the reality of the H.U.M. camp. Perched in the foothills of the Himalayas, the camp was brimming with overweight teen-age Saudis who had come to get in shape at the Islamic equivalent of a fat farm. There was no live ammunition at the camp, and most of the three-week basic-training program consisted of calisthenics.

The camp was across the road from a Pakistani military base, and Pakistani intelligence officers regularly came to deliver instruction, Lindh told Gunaratna. His growing doubts about the purity of the cause were compounded when, during his basic training, he glimpsed a doctored map in the officers’ quarters. Instead of showing Kashmir as an independent Islamic state, the map pictured Kashmir annexed to Pakistan. “It was not an Islamic struggle, it was a political struggle,” Lindh told Gunaratna. “I became disillusioned by the training. H.U.M. had no clear goal, no clear answer about whether Kashmir was to become independent. My preoccupation was that Kashmir become independent. I didn’t want it to join Pakistan, because Pakistan is a secular state.” He dropped out.

Days after abandoning the Kashmiri cause, Lindh decided to join the jihad in Afghanistan. In the Pakistan madrasahs, he told Gunaratna, he had been steeped in stories about the mujahideen’s glorious victories over the Soviets in the nineteen-eighties. Their brutal, puritanical successors, the Taliban, were venerated as upholders of Islam; their remaining foes, the Northern Alliance, were portrayed as cruel oppressors. “I had heard reports of massacres, child rape, torture,” he later told the court. He was excited to learn that the Taliban had almost succeeded in defeating the Northern Alliance, and he was eager to help them turn all of Afghanistan into a theocracy.

In June, when Lindh crossed the Khyber Pass into Afghanistan, Pakistani border guards shot at him with machine guns. He told Gunaratna that his original plan was to go directly to the Taliban’s “front line.” Had he succeeded, he might have sidestepped the offense that links him most closely to Al Qaeda. But, since he spoke no Urdu, Dari, or Pashto, the Taliban recruitment office he reported to in Kabul told him he would have to join a non-Afghan, Arabic-speaking unit. This group, Al Ansar, required that Lindh go through basic training again before joining the front. Al Ansar, which means “the supporters,” was founded to help fight the Soviets; since those early days, it had been funded in part by Osama bin Laden’s fortune. (Al Ansar is not affiliated with Ansar al-Islam, a militant group in Northern Iraq.)

That month, Lindh said, he checked into an Al Ansar training camp west of Kandahar, in southern Afghanistan. The camp’s name was Al Farooq. Lindh has told government investigators that the days began at three-thirty in the morning, with a call to wash. At five-thirty, there was prayer and Koran reading until sunrise. At seven-thirty, there was morning exercise. Breakfast was at eight-thirty, followed by classes in warfare. Students learned how to handle various weapons, including rocket-propelled grenades; most of the focus, however, was on guns. (“It must have been boring,” Sonn suggested to Lindh. “Not really,” he replied. “I’d never seen guns before.”) Then there was lunch, more classes, chores such as fetching water from a well, more classes, evening speeches, dinner, and more prayers. The bedtime roll call was at nine.

The government’s indictment describes Al Farooq as an “Al Qaeda facility,” and charges that Lindh went there “knowing that America and its citizens were the enemies of Bin Laden and Al Qaeda and that a principal purpose of Al Qaeda was to fight and kill Americans.” Paul McNulty, the United States Attorney whose office prosecuted the case, contended in a recent interview that it would have been hard for Lindh not to know that “it was a place where Al Qaeda operatives trained.”

Lindh admits that he knew that bin Laden gave money to Al Farooq. But he says he didn’t know much about Al Qaeda, nor did he perceive that the boot camp had been infiltrated by bin Laden’s organization. Lindh also claims that he never heard the words “Al Qaeda” at the camp. This sounds unlikely, but Gunaratna, who was familiar with the structure of the Al Farooq camp, found Lindh’s claims plausible. “There were two kinds of courses at Al Farooq: Al Qaeda training, to fight civilians, and military training, to fight the Northern Alliance,” he told me. “Lindh took only the military training.” Bruce Hoffman, a terrorism expert at the Rand Corporation, in Washington, D.C., agreed with this analysis. “These camps were waging a traditional war against the Northern Alliance,” he said. “Seventy thousand people were trained in general warfare at these camps, but perhaps only a tenth received advanced terrorist training.” McNulty is more skeptical. “Sure, it’s in the interests of the defense to suggest there was a distance between them, but the relationship between the Taliban and Al Qaeda is what it is,” he said.

Perhaps the indictment’s gravest charge was that Lindh had advance knowledge of murderous assaults like those on New York and Washington. At Al Farooq, the indictment states, Lindh learned that bin Laden “had sent forth” around fifty people to carry out twenty suicide terrorist operations against the United States and Israel. Lindh denies this, claiming that a government investigator garbled a story that he had told him. It was after September 11th that a Taliban supporter fighting alongside him against the Northern Alliance talked menacingly about future attacks. Lindh said he never heard any talk at Al Farooq about terrorists attacking America.

McNulty scoffed at this, noting that Osama bin Laden paid three visits to Al Farooq during the seven weeks Lindh was training there. “How could he not know that these people had a bone to pick with America?” he asked.

Regarding bin Laden’s presence at Al Farooq, Lindh said that he was unsure what to make of him. He said that he had heard praise of bin Laden’s role as a mujahideen warrior against the Soviets—but also rumors about his role as the terrorist behind the bombings of the U.S.S. Cole and America’s embassies in East Africa. Lindh’s classmates back in Yemen, however, had assured him that these allegations weren’t true. Lindh was prone to discount terrorism accusations against Muslims, even if it required accepting wild conspiracy theories. In a letter to his mother written after the 1998 embassy bombings, Lindh said that the attacks “seem far more likely to have been carried out by the American government than by any Muslims.”