When he heard last week that enemy combatant and alleged “dirty bomber” Jose Padilla had finally been charged in open court after being held for three years ina Hanahan naval brig, James Youseff Yee was a little less than philosophical.

“What I saw on the news was that, clearly, the Bush Administration justwants to avert a showdown with the Supreme Court,” says Yee from his home in Tacoma, Wash. “I definitely would have liked to see how the Supreme Court would have ruled on the issue of presidential executive power to hold a U.S. citizen as an enemy combatant.”

Yee, understandably, takes a dim view of the administration’s war on terror, having had his name dragged through the mud after he was arrested at a Florida naval air station two years ago by federal agents. Subsequently, he was accused in the press of aiding and abetting terrorists imprisoned at Camp X-Ray in Guantanamo Bay, Cuba, where the West Point grad had been serving as a Muslim chaplain.

Manacled and forced to wear sightless goggles and ear-muffs on his flight to Charleston, Yee, like Padilla, was held at the converted naval brig in Hanahan.

“I was expecting to have a burlap hood pulled over my head, like the ones I’d seen on those prisoners brought to Guantanamo where that tactic started,” says Yee, who will be in town to speak to a local Amnesty International chapter on Wed., Dec. 7.

Apparently living on the same floor as Padilla, Yee had no idea where he was until he received a prison guidelines booklet that had the word “Charleston” printed in its margins.

Under 24-hour surveillance and left with little more than a copy of the Koran, Yee was not allowed by some guards to keep even toilet paper in his cell. He was forced to be shackled naked into a “three-piece suit” of handcuffs, leg irons, and chains before being allowed to walk down the hall in a towel for a shower — but not before a full strip search.

Even though he was able to arrange Muslim-appropriate meals for the “terrorists” held at Guantanamo, Yee did not receive food in keeping with his religious tenets while in the brig here. Nor could he figure out which way Mecca was, despite a sliver of a window at the top of his tiny cell (“I’m 5-foot-6, and there was just barely enough room for me to do sit-ups across the width of the cell”).

Yee was released after 76 days in solitary confinement, and charged with mishandling classified documents. All charges were later dropped, with even minor infractions expunged from his record.

Today, out hawking his new book, For God and Country: Faith and Patriotism Under Fire, he is still fighting for an apology from the military.

Padilla, on the other hand, is still facing a world of hurt.

A sealed indictment opened in federal court last week charges the former Chicago gang member with providing and conspiring to provide “material support to terrorists, and conspiring to murder individuals overseas. …. [having] travelled overseas to train as a terrorist with the intention of fighting in ‘violent jihad,'” according to a speech made last week in Florida by U.S. Attorney General Alberto R. Gonzales.

Padilla has been held in the brig for three years without being charged, according to Gonzales, because of intelligence gathered under the provisions of the USA PATRIOT Act, which critics contend allows the government too much free rein in searching for terrorists.

“It would be interesting to know if I was held under the Patriot Act,” says a wistful Yee, who claims he has encountered roadblock after roadblock in his attempts to get back personal belongings confiscated by federal authorities in 2003.

“We are living in historical times where we are seeing the erosion of our civil liberties,” says Yee.

“My experience, born of what I’ve gone through with my case, is that the current approach to fighting terror from within our own borders is a threat to ordinary citizens’ civil liberties,” says Yee, who was ordered incarcerated by the same man, U.S Army Maj. Gen. Geoffrey Miller, who was transferred to run all the military prisons in Iraq, including Abu Ghraib, after reports of prisoner abuse surfaced there.

(According to USA Today, Miller also “recommended interrogation techniques that military lawyers said had to be modified to comply with the Geneva Conventions on treating prisoners of war” after visiting Abu Ghraib.)

“That’s why we see the controversy over the Patriot Act and what it entails: the material witness statute, enemy combatant status, and extraordinary rendition.”

Extraordinary rendition, or the U.S. government’s alleged practice of “outsourcing the torture of witnesses to countries that allow it,” is just one of the many reasons Stewart Flood wants to see the act, otherwise known as the Uniting and Strengthening America by Providing Appropriate Tools Required to Intercept and Obstruct Terrorism Act of 2001, repealed.

Flood, the former head of the now-defunct city of Charleston Republican Party, has joined forces with an unlikely ally, Charleston’s über-liberal protestor Merrill Chapman, to form a group whose main mission will be to get Charleston County Council to file a resolution opposing the Patriot Act.

“Our opposition to the act has nothing to do with the war,” says Flood, now a member of the local Libertarian Party. In fact, he says, all other issues are off the table when it comes to fighting the Patriot Act, to help keep the group, which had its first meeting this week, focused.

Flood, who drove 1,800 miles round-trip for Thanksgiving to avoid a potential strip search before getting on a plane or a train, finds it reprehensible that the federal government or its agents, “can go into some citizen’s home or business, search it, and seize records without having to tell you they’ve been there thanks to the Patriot Act.”

Flood, likening the current state of civil liberties to the clampdown pictured in the Bruce Willis-Denzel Washington movie The Siege, wonders how many constitutional amendments the act “doesn’t break.”

Chapman claims there are 389 resolutions in 43 different states, including seven statewide resolutions against the act. “Columbia is working on one, Beaufort is working on it, and Aiken is working on it, too,” she says.

Chapman hopes that federal authorities will hear the message of “Patriot Act-free zones” and listen to the people. “Who knows, maybe our leaders in Washington, D.C., will listen to the American public.”