That fate apparently led him to fight for the Taliban in the name of terrorist warlord Osama bin Laden, and by the weekend it had left him on a bloody gurney in the Northern Afghan fortress of Kala Jangi.
And it was there that his parents back in Marin saw their 20-year- old son for the first time in six months -- on TV, in broadcasts as he proclaimed his support for the Taliban and for the Sept. 11 terrorist attacks.
They told reporters they couldn't match up the televised image of the grubby, half-starved, wounded soldier now in U.S. custody with the shy, deeply spiritual boy who lived in the comfort of Marin County.
"John is a very sweet kid, devoted, religious, devoted to his religious conversion . . . a good boy," Walker's father, Frank Lindh, said last night in a televised interview. "I want to give him a hug, and maybe a little kick in the butt for not asking my permission to go to Afghanistan."
As for Walker's televised statements from Kala Jangi on Sunday that he was a "jihadi," or holy warrior, and that he supported the Sept. 11 terrorism massacres in America, Lindh said he was mystified. Despite hearing the words from his son's lips on TV, he insisted, "There's no indication he's done anything wrong."
Lindh noted that his son had been interviewed right after being pulled out of a flooded dungeon in a fort where he and others had been in a fiery standoff with U.S. and Northern Alliance forces for days -- and that anything he said at that point should be taken with a grain of salt.
"I don't think he was thinking straight at that moment," Lindh said. "I don't think anyone could think straight at that moment.
"I just ask people to have some mercy."
The transformation of John Phillip Walker Lindh -- in recent years he dropped his father's last name in favor of his mother's -- was equally confounding for Walker's friends. The same is true for leaders at Tamiscal High School in Larkspur, where he was so bright he managed to graduate at 16, and even for those who helped him make his conversion to Islam four years ago.
"He is quiet and soft-spoken and humble," Abdulla Nana, a 23-year- old fellow Muslim who said he was a "close friend," told The Chronicle. "He was a gentle person. I wouldn't have expected him to go and fight there."
Nana studied and prayed with Walker at the Islamic Center and Mosque of Mill Valley beginning in 1997. He helped his friend blossom from a spiritually questing teen to a Muslim so devout he never went out without his traditional thobe, or Islamic cloak.
"As a convert, he was an example of how to behave," he said. "We looked up to him because of his dedication to Islam."
How that dedication led to apparently carrying an AK-47 and bearing the adopted Arabic name of Abdul Hamid, in battle against the homeland for which he still holds a passport may be fuzzy -- but there were early indicators that he might have been heading that way.
For instance, he was studying Arabic language and culture in Yemen last year when the U.S. destroyer Cole was bombed, reportedly by bin Laden operatives, and he told his father the attack was a "justified response," according to Newsweek.
"It was clear he had developed a different point of view," Lindh told the magazine.
And then there was Walker's disappearance about six months ago in Pakistan, where he had gone to study native languages and the Koran. The northwest frontier he went to, like Yemen, is rife with terrorist training camps. And after he stopped corresponding with his parents by e-mail, they became so worried they passed his photo around at mosques in San Francisco.
Walker had occasionally worshipped in the city, and they thought maybe someone knew where he was, friends said. But they had no luck.
What nobody back home knew, evidently, was that -- according to Walker's interviews Sunday -- he was training with bin Laden's forces and later fought with them for the Taliban.
Even now, his mother, Marilyn Walker -- who is separated from his father -- and others believe that if he was fighting for bin Laden, he was brainwashed.
"I think he was there seeking spirituality and wasn't a terrorist," said family friend Bill Jones. "It was a youthful indiscretion."
From the moment he began converting to Islam, it was clear Walker was going to tread a singular path far from the mainstream.
He was born in the Washington, D.C., area, his father was an attorney for the U.S. Department of Justice, and his mother was a home health aide, according to friends and press reports. He was named after former Beatle John Lennon and has a younger sister and an older brother.