More than anything about his arrest and detention, former U.S. army captain James Yee remembers the shackles.

Placed on his wrists and ankles, the manacles were secured to a chain wrapped around his waist. Back at the Guantanamo Bay, Cuba, prison camp, where Yee worked as a Muslim military chaplain, the restraint was known as a "three-piece suit" and commonly used to hobble the most dangerous of America's enemies.

"At that point, I clearly understood they were treating me like an enemy combatant," Yee recalls. "That's how prisoners were taken around in camp, and I was shackled just like them. That was the scariest part."

It was September 2003 and Yee, a West Point graduate with a spotless military record, had just been arrested at Jacksonville, Fla., after returning to the U.S. mainland for a two-week leave.

The allegations were serious, and especially lurid in post-9/11 America.

Investigators suspected Yee of being part of an espionage ring among Muslim-American soldiers at Guantanamo. In leaks to the media, they said Yee was being jailed on suspicion of stealing classified information from Guantanamo and aiding the enemy, a crime potentially punishable by death.

For 76 days, Yee was imprisoned, sometimes blindfolded and in isolation, at a military brig in Charleston, S.C., while investigators tried to build their case against him. They couldn't do it.

Six months after Yee was identified in the U.S. media as a possible traitor, an embarrassed Pentagon withdrew all criminal charges against him, including mishandling classified information, after failing to show documents in Yee's possession were in any way secret.

He was never charged with spying, never charged with sedition.

In a final act of exoneration, an army general even dismissed minor convictions for adultery and misuse of a government computer, non-criminal charges that were embarrassing but entirely unrelated to national security.

"It was such a gross miscarriage of justice," says Yee, now living in Olympia after receiving an honourable discharge with commendation for "exceptionally meritorious" service.

"I was wrongfully accused. I was unjustly imprisoned, treated harshly," he says. "There was no classified information, but they held me for 76 days. That's not justice."

Five years after the Sept. 11, 2001, terror attacks, the military's failed case against Yee has become part of a much broader national debate about President George W. Bush's tactics in the war on terror, and the impact they've had on civil liberties and the rule of law in a nation that prides itself on both.

With the nation united behind him in the months after 9/11, Bush approved several extraordinary measures he believed necessary to prevent another attack, but which also tested the limits of U.S. law. They included authorizing the indefinite detention of U.S. citizens without charge, the denial of Geneva Convention rights to foreign detainees, the extraordinary rendition of terror suspects, wiretapping of domestic communications without warrant, and the secret collection of personal library, Internet and banking records.

For administration supporters, the clearest evidence the tough tactics have worked is that America has not suffered another terrorist attack on home soil, but critics maintain the cost to the country has been too high and that, in the zeal to prevent another 9/11, the Bush administration's actions have eroded core American values embodied in the final words of the Pledge of Allegiance: With liberty and justice for all.

"What is at stake is whether we want to remain that country of our ideal," says Matthew Robinson, a criminologist at Appalachian State University and frequent lecturer on the USA Patriot Act, one of the administration's most prominent counterterrorism tools.

Robinson says "there's no question" the civil liberties of ordinary Americans have suffered in the post 9/11 era.

"Sometimes it's hard to say exactly how much because of the secretive nature of everything the government is doing," he said.

"No one knows whose phone has been tapped. No one knows whether their e-mail has been read or whether their list of library books has been checked. No one knows whose bank accounts have been accessed by the Treasury Department."

The Justice Department says the measures have helped law enforcement disrupt more than 150 terror threats and cells, track hundreds of terror suspects and led to the removal from the U.S. of more than 500 people linked to the Sept. 11, 2001, investigation.

Bush has repeatedly insisted the investigative measures he authorized are used only to track suspected terrorists, not to troll through the private records and conversations of ordinary citizens.

For the most part, polls have suggested Americans fearful of another major attack supported the president's actions, especially in the first years after 9/11. Andrew McCarthy, senior fellow at the Washington-based Foundation for the Defence of Democracies, says Bush has acted within constitutional powers that give U.S. presidents "the power capable of meeting any conceivable threat" to the country.

"I think most people realize that, to the extent government is invading their privacy, it really is for the most part because it is trying to protect us from the possibility of threats," McCarthy said.

"It's an unavoidable situation."

Civil libertarians, though, cite cases where Americans have been wrongfully accused or where courts have taken action to rein in the administration.

In 2004, the FBI arrested U.S. citizen Brandon Mayfield, a lawyer and convert to Islam, after mistakenly matching his fingerprints against those of a suspect in the Madrid train bombings.

In 2005, amid several legal challenges, the Justice Department agreed to criminally charge U.S. citizen Jose Padilla, accused of plotting to detonate a dirty bomb, after holding him without charge as an "enemy combatant" for more than a year.

In June, the U.S. Supreme Court ruled Bush overextended his authority by denying terror detainees Geneva rights and by establishing special military tribunals at Guantanamo Bay without seeking congressional approval.

"Nobody is talking about taking away the government's authority to wiretap terrorists or detain terrorists," says Jameel Jaffer, deputy director of the American Civil Liberties Union's national security program.

"But the system of checks and balances that many Americans value has been seriously eroded over the past five years."

In addition to the higher profile tactics in the war on terror, Jaffer says ordinary Americans are subject to unjustified investigation through the use of special "national security letters." The Federal Bureau of Investigation issues about 30,000 national security letters a year, which allow agents to secretly demand personal information about Americans from libraries, Internet providers and other business that collect private data.

The reason Americans haven't protested against the anti-terror tactics more vigorously, says Jaffer, is "people are always willing to trade other people's freedoms for their own security."

Just as administration critics acknowledge government tactics have had success breaking up some plots, the president's supporters admit the consequence of aggressive investigations is that mistakes are made along the way, with innocent people wrongly accused.

It's a necessary consequence of shifting to a "prevention paradigm" that encourages law enforcement to prevent attacks rather than investigate them after the fact, McCarthy said.

"Your evidence is going to be, by nature, more ambiguous. You are going to be casting a wider net because you are trying to prevent things," he said.

"When you are doing something that is more difficult, and harder to prove, and less exact, you have to accept the fact there are going to be mistakes."

That's cold comfort to Yee, who said he believes he was victimized because of a post-9/11 atmosphere that fostered suspicion of Muslims.

Two days before he was arrested on Sept. 10, 2003, Yee had received the best officer evaluation report of his career. His superior officers, seeking to demonstrate religious diversity in the U.S. military, regularly publicized his work as a Muslim chaplain at Guantanamo.

But Yee came under suspicion for holding Friday night meetings with other Muslim soldiers and some officers perceived him as being too concerned about the treatment of detainees.

"The case against him was a toxic combination of overzealousness, hysteria and, I would say, prejudice," says Eugene Fidell, a civilian lawyer who represented Yee. "You could view the whole thing as a smear campaign, because when push came to shove, they abandoned the case."

More than 21/2 years after the military's case collapsed, Yee is still struggling to rebuild his life.

"They arrest people and ask questions later," he says. "It was my job to advocate for diversity and tolerance and the humane treatment of prisoners. Because I defended American values effectively, I was targeted."

Yee has earned a living on the lecture circuit and through TV appearances as a commentator on Guantanamo and military justice issues, but he still finds himself the subject of suspicion.

In July, he was questioned for two hours by customs officials after a trip to Vancouver to see Cirque de Soleil.

"I have accepted the fact that I will be the subject of surveillance for the rest of my life," Yee said.

Despite his ordeal, Yee insists he has not lost faith in his country.