This should be our Nuremburg, the defining trial of the 9/11 era and a fitting coda to it.

Unfortunately, the U.S. government appears to be on the verge of squandering this opportunity, and with it, the best, and perhaps only, chance for the public to understand not only how the attacks came to be, but why Mohammed waged a relentless war against America and how we might stop the next would-be terrorist mastermind.

The problems lie within the reformed military-tribunal system that the Obama administration put in place after losing its fight for a civilian trial in New York. Political compromises have resulted in a flawed military commissions process that from outward appearances is not only rigged against the defense, but hyper-choreographed, censored and hermetically sealed.

“The process is designed to achieve a conviction, and to do it with as little revelation as humanly possible, but with the veneer of due process and justice,’’ said one participant who said restrictive gag orders prohibited him from talking publicly. “You’re talking about the most heinous crime ever, and we’re going to afford them less due process, less discovery, less of everything than we would the guy who shoplifted a pack of gum from CVS.’’

Obama administration officials say their reformed military commissions system is a vast improvement over the Bush administration’s version, which Obama moved to shut down on his first day in office in 2009.

Defense lawyers disagree, and insist they have been hamstrung in their efforts to mount the kind of aggressive defense needed to do their jobs including full and unfettered access to evidence, witnesses and even the accused themselves.

Four of the five legal teams had so few of their key players in place in recent months that they did not file the “mitigation submissions’’ that the government said it needed to decide which of the five men should face the death penalty and other key issues, such as whether to try them together or individually. They recently filed motions asking that the charges be thrown out because of fatal flaws in the system, which they say make it impossible for them to defend their clients.

“It’s window dressing,’’ Mohammed’s defense lawyer, David Nevin, said of the government’s improvements. “I am not all satisfied that it is a fair process. In fact, it is not a fair process.’’

Many of the defense lawyers have quit out of frustration or for other personal reasons stemming from the many delays in the process. Only a few have been there long enough to even begin to understand their clients’ case, not to mention the convoluted military commission process.

And they say they will be unable to effectively challenge confessions obtained when their clients were coercively interrogated in the CIA’s black site prisons, if they can broach the subject at all. This is important for the four men accused of helping Mohammed with the logistics of the plot. Several claim they have been wrongly accused, tortured into confessing, or both.

It is also important with regard to Mohammed, who confessed to dozens of plots while being waterboarded 183 times, and has said he may plead guilty even before the trial begins. Few U.S. counterterrorism officials believe all of his often boastful confessions, and it is important for the public to hear what, exactly, evidence the government has with regard to what he did and didn’t do, and whom he might have been protecting.

The team of Defense and Justice Department officials overseeing the military commission process, and the presiding judge, should quickly address the defense lawyers’ complaints, or a proceeding that some call “The Trial of the Century’’ will be delayed further by legal wrangling — and forever tainted by accusations of being unfair.

A full, fair and transparent trial, above all, will benefit the public. There is much the public doesn’t know about Mohammed, including the details of how he devised the plot, convinced bin Laden to let him do it and then orchestrated it “from A to Z,’’ to use his own words. It was Mohammed who masterminded dozens of other plots and attacks, some while staying a step ahead of the largest-ever criminal manhunt.

Mohammed, not bin Laden, was the one who traveled the world as a kind of “Johnny Appleseed’’ of terrorism, establishing alliances and creating a network of cells and lieutenants that in some cases remains today. And it was Mohammed who personally recruited young jihadist prospects much like a baseball scout, many of them Westerners, tapping into their grievances to turn them to his cause.

The U.S. government has kept the details of what Mohammed did — and how and why he did it — hidden in its most classified files since his capture in Pakistan nine years ago. The government should set the record straight on that, because there is an important lesson to be learned from the largely untold tale of Khalid Sheikh Mohammed: It isn’t some monolithic group like al-Qaida that poses a continuing threat, it’s the one intelligent and energetic person who can emerge from nowhere and orchestrate a 9/11 while the world focuses elsewhere.

To that end, the government should declassify as much evidence as possible, and explain how it obtained it. It should call numerous witnesses to testify, especially since the one who has been publicly identified, Majid Khan, claims he was tortured while in CIA custody overseas.

Instead of limiting access to a few closed-circuit TVs, it should consider televising the proceedings. It should ensure that censorship is minimized, and used only to protect intelligence sources and methods, not to save the government from embarrassment. And it should let Mohammed and the others testify at length on their behalf if they so desire.

By doing so, the Obama administration will be able to say it did its best to put on the kind of civilian trial it has wanted all along, and one with a similar outcome to that of the al Qaida members charged with blowing up two U.S. embassies in Africa in 1998.

Those of us who witnessed that trial in Manhattan in 2001 saw the defendants squirm in their chairs as prosecutors introduced mountains of evidence against them. We saw eyewitnesses point the finger at the accused, and surviving victims glare at them from the pews.

We heard from the terrorists themselves, and learned a lot about why they did it, about how terrorist networks operate and about what might be done to stop people like them. And when the jury convicted them, there was no question that justice was done.

Assistant Attorney General Thomas Perez threw down the gauntlet for Arpaio at Thursday’s press conference, giving him until Jan. 4, 2012,  to accept DOJ’s measures to take “clear steps toward reaching an agreement with the Division to correct these violations in the next 60 days,” or face a lawsuit.  Perez expressed DOJ’s willingness ”to roll up our sleeves and build a comprehensive blueprint for reform of MCSO,” adding, “if the will exists” on Arpaio’s end.

That’s a big if. Now a real clock may be finally ticking for the countdown of the nearly 20-year reign of America’s self-proclaimed “Toughest Sheriff.”

One federal department is not even waiting: Within hours of the DOJ announcement, the Department of Homeland Security terminated Maricopa County’s access to immigration status data under the federal Secure Communities program.

The announcement comes amid growing calls for Arpaio’s resignation, in the aftermath of allegations that his department mishandled hundreds of sex crime reports in the Phoenix area township of El Mirage.

Rep. Raul Grijalva was the first to call for Arpaio to step down.

“Mr. Arpaio might love headline-grabbing crackdowns and theatrical media appearances,” the Tucson Democrat said last week, “but when it comes to the everyday work of keeping people safe, he seems to have lost interest some time ago.”

A few days later Rep. Ed Pastor, who represents Maricopa County in Congress, endorsed a call for Arpaio’s resignation. So did nine state legislators. Even Cafe Con Leche Republicans, a national organization, released a statement this week that “Arpaio has disgraced his office and the Republican Party.”

On Monday, religious leaders from 14 mainline denominations called on the attorney general to release its findings and take “immediate action to quell the growing human rights crisis in Arizona,” a reference to Arpaio’s law enforcement regime.

Citizens for a Better Arizona, a new group, which organized the successful recall of Tea Party leader and former state Senate president Russell Pearce in November, organized a major turnout at the Maricopa County board of supervisors meeting on Wednesday to call for Arpaio’s resignation.

“This is a very important day for Maricopa County,” County  Supervisor Mary Rose Wilcox, a critic of Arpaio, told supporters following the release of the report. “It’s a day many of us have been awaiting. Let this be the end of Arpaio. Give us a better criminal justice system.”

The 79-year-old sheriff has rarely failed to express disdain for federal oversight, especially from the Obama administration. Last week, Arpaio couldn’t resist tweeting his glee about a dubious report in the Globe tabloid newspaper that his “Cold Case posse” investigation of President Obama’s birth certificate had the first lady “in a panic.”

Two years ago, after Department of Homeland Security chief Janet Napolitano had also announced her intentions to terminate the DHS cooperation with Arpaio’s office, Sheriff Arpaio appeared on the Glenn Beck show and openly mocked federal authority.  Arpaio claimed that local and state laws allow him to target “some people who have an erratic, scared … whatever … if they have their speech, what they look like, if they look like they come from another country, we can take care of that situation.”

The DOJ report concluded that Arpaio engaged in racial profiling.

“Our investigation uncovered substantial evidence of the kind identified by the Supreme Court in Arlington Heights,” the report noted, “showing that Sheriff Arpaio has intentionally decided to implement his immigration program in a manner that discriminates against Latinos.”

The report added a telling detail about Arpaio’s effectiveness as a law enforcement officer. While his operations involved “the most egregious racial profiling in the United States,” according to one expert, “enforcement actions rarely result in human smuggling arrests.”

Another law enforcement officer last week levied a similar charge against Arpaio on the botched sex crimes investigations. Bill Louis, former assistant police chief in  El Mirage, wrote an Op-Ed in the Arizona Republic declaring that ”Sheriff Joe Arpaio failed these victims. At this point there is little that can be done to undo the harm they have endured.”

Not that criticism or outrage has ever moved Arpaio to veer from the style that has made him a hero to some conservatives: his high-profile immigrant sweeps, his order that prisoners had to wear pink underwear, or his reality TV exploits. Last spring, he simply shrugged off  calls for his resignation over allegations of his department’s misuse of $100 million.

Four aged right-wingers apparently plotted to carry out a mass murder based on the plot of a thriller written by frequent Fox guest Mike Vanderboegh. They planned to “save this country” by attacking Washington, D.C., and Atlanta with ricin and botulinium toxin. And they were targeting the government:

What was the ostensible purpose of all this killing? Saving the country of course. “There is no way for us, as militiamen, to save this country, to save Georgia, without doing something that’s highly, highly illegal: murder,” Thomas reportedly said. “When it comes time to saving the Constitution, that means some people have got to die.” The FBI also alleges that “Thomas, Roberts and others discussed the need to obtain unregistered silencers and explosive devices for use in attacks against federal government buildings and employees, as well as against local police.”

The group also had a “bucket list” of politicians and members of the media that they planned to kill, which seems to be a misreading of the “bucket list” concept. Two of the men bought “what they believed was a silencer and and unregistered explosive” from an FBI informant, as well. They also — with the informant — drove to Atlanta to “scope out” IRS and ATF buildings.

The “good news,” I guess, is that now the Justice Department is carrying out the same ridiculous stings on old Christian guys that it regularly carries out on young Muslim guys. Because let’s be honest, we have no way of knowing whether these four guys would’ve actually acted on their anti-government beliefs if they hadn’t been led to action by the “informants.” They met at a Waffle House and called themselves “the covert group.” They range in age from 65 to 73. How much of a real threat could they possibly have been? How much of a role did the “informant” play in pushing the men toward formulating an actual terror plot instead of just grumbling fantasies of revolution over omelets?

They may have been able to manufacture ricin — one of the men “used to work as a lab technician for a U.S. Department of Agriculture agency known as the Agricultural Research Service,” according to ABC News — but it’s unclear how practical ricin is as a chemical weapon. A terrorist needs tons of ricin to kill people through mass dispersal. Ricin is what terrorists turn to when they fail to make anthrax.

This looks like the same “entrapment in all but name” approach to fighting terror that the Justice Department has been pursuing against American Muslims for years. What will be interesting to see is whether the entrapment defense works any better for a gang of four elderly white guys than it does for teenagers with names like “Hosam Maher Husein Smadi.”

This is a big leap for Richard Cohen, a writer who hates democracy and defended Dick Cheney’s torture regime as recently as 2009. (2009!)

So he begins by pointing out that he cheered the death of Anwar al-Awlaki:

A little “yippee” emitted from me when I heard the news. Awlaki was a traitor to his country and its values. He was allegedly a senior recruiter for al-Qaeda and was linked to the Fort Hood shooting suspect Nidal Malik Hasan as well as other attempted terror acts. Awlaki was not shy about his activities, and so they, not to mention his allegiance, were not in question.

But! This whole targeted killing of an American citizen thing is sort of problematic, according to the Constitution and “our founding ideals.”

The American Civil Liberties Union has criticized Awlaki’s killing. But so far, the only politician of note to do so is Rep. Ron Paul, the Republican presidential candidate with a touching reverence for the Constitution as written. “Al-Awlaki was born here; he’s an American citizen. He was never tried or charged for any crimes,” he exclaimed. Paul, though, gets dismissed as a constitutional kvetch.

I do not share Paul’s indignation, but I do his dismay. Something big and possibly dangerous has happened . . . in secret. Government’s most awesome power — to take a life — has been exercised on one of its own citizens without benefit of trial. A guy named Barron and another named Lederman apparently said it was okay. Maybe it was. But I’d sure like to hear the attorney general or the president explain why.

(This Barron guy and this Lederman guy are actually very prominent attorneys known, ironically, for their particularly sharp criticisms of the Bush administration’s abuses of presidential war powers, but I wouldn’t expect a man who’s had a political column at Washington primary newspaper for 35 years to actually know anything at all about what he writes about, ever.)

But the last line gives the game away: Richard Cohen finds the idea of the president having the power to unilaterally order the execution of an American citizen absurd on its face. This puts him in league with people like Ron Paul and the ACLU. He does not wish for that sort of company. So he is begging for some grown-up Washington person to explain why this is all totally OK. He would like the president to reassure him. Won’t somebody please reassure Richard Cohen that it’s OK for the president to assassinate people?

Needless to say, none of the government officials responsible for this abuse of a U.S. citizen on American soil has been held accountable in any way.  That’s because President Obama decreed that Bush officials shall not be criminally investigated for War on Terror crimes, while his Justice Department vigorously defended John Yoo, Donald Rumsfeld and other responsible functionaries in civil suits brought by Padilla seeking damages for what was done to him. 

As usual, the Obama DOJ cited national security imperatives and sweeping theories of presidential power to demand that Executive Branch officials be fully shielded from judicial scrutiny (i.e., shielded from the rule of law) for their illegal acts (the Obama DOJ: ”Here, where Padilla’s damage claims directly relate, inter alia, to the President’s war powers, including whether and when a person captured in this country during an armed conflict can be held in military detention under the laws of war, it would be particularly inappropriate for this Court to unnecessarily reach the merits of the constitutional claims” (emphasis added)).  With one rare exception, federal courts, as usual, meekly complied.  Thus, a full-scale shield of immunity has been constructed around the high-level government officials who put Padilla in a hermetically sealed cage with no charges and then abused and tortured him for years.

The treatment Padilla has received in the justice system is, needless to say, the polar opposite of that enjoyed by these political elites.  Literally days before it was required to justify to the U.S. Supreme Court how it could imprison an American citizen for years without charges or access to a lawyer, the Bush administration suddenly indicted Padilla — on charges unrelated to, and far less serious than, the accusation that he was A Dirty Bomber — and then successfully convinced the Supreme Court to refuse to decide the legality of Padilla’s imprisonment on the grounds of “mootness”  (he’s no longer being held without charges so there’s nothing to decide). 

At Padilla’s trial, the judge excluded all evidence of the abuse to which he was subjected and even admitted statements he made while in custody before he was Mirandized.  Unsurprisingly, Padilla was convicted on charges of “supporting Islamic terrorism overseas” — but not any actual Terrorist plots (“The government’s chief evidence was an application form that government prosecutors said Mr. Padilla, 36, filled out to attend an Al Qaeda training camp in Afghanistan in 2000″) – and then sentenced to 17 years in prison, all above and beyond the five years he was imprisoned with no due process.

Not content with what was done to Padilla, the Bush DOJ – and then the Obama DOJ – contested the sentence on appeal, insisting that it was too lenient; Padilla also appealed, arguing that the trial court made numerous errors in excluding his evidence while allowing the Government’s.  Yesterday, a federal appeals panel of the 11th Circuit issued a ruling, by a 2-1 vote, rejecting each and every one of Padilla’s arguments.  It then took the very unusual step of vacating the 17-year-sentence imposed by the trial court as too lenient and, in effect, ordered the trial judge to impose a substantially harsher prison term:

Padilla’s sentence is substantively unreasonable because it does not adequately reflect his criminal history, does not adequately account for his risk of recidivism, was based partly on an impermissible comparison to sentences imposed in other terrorism cases, and was based in part on inappropriate factors . . . .

As the dissenting judge explained, this decision is extraordinary because trial judges — not judges sitting afterward on appeal — are the ones who hear all the evidence and thus have very wide discretion to determine the appropriate sentence.  But more so, in this case, a sentence less than the full maximum was warranted because “the trial judge correctly concluded that a sentence reduction is available to offenders who have been subjected to extraordinarily harsh conditions of pre-trial confinement.”  About that point, the dissenting judge documented:

Padilla presented substantial, detailed, and compelling evidence about the inhumane, cruel, and physically, emotionally, and mentally painful conditions in which he had already been detained for a period of almost four years. For example, he presented evidence at sentencing of being kept in extreme isolation at the military brig in South Carolina where he was subjected to cruel interrogations, prolonged physical and mental pain, extreme environmental stresses, noise and temperature variations, and deprivation of sensory stimuli and sleep.

In sentencing Padilla, the trial judge accepted the facts of his confinement that had been presented both during the trial and at sentencing, which also included evidence about the impact on one’s mental health of prolonged isolation and solitary confinement, all of which were properly taken into account in deciding how much more confinement should be imposed. None of these factual findings, nor the trial judge’s consideration of them in fashioning Padilla’s sentence, are challenged on appeal by the government or the majority.

Thus: American officials who are responsible for this “inhumane” and “cruel” abuse of detainees act with full impunity, as usual.  Those who are its victims are not merely denied all redress (though they are), and do not merely have the courthouse doors slammed in their faces in the name of secrecy, national security and presidential power (though they do), but they are also mercilessly punished to the fullest extent possible.

It should be said that part of what happened here is just the typical politicization of the judiciary, as the two-judge majority was comprised of a hard-core right-wing Reagan/Bush 41 appointee from Alabama (Joel Dubina), while the other was one of Bush 43′s most controversial appointees, the former Alabama Attorney General who was filibustered by the Democrats and allowed onto the bench only by virtue of the “Gang of 14″ compromise (William Pryor).  Meanwhile, the dissenting judge was born in Mexico to Syrian parents and, after moving to Miami at the age of 6, became the first female judge (as well as the first Hispanic and Arab American judge) on the Florida Supreme Court (rising to Chief Justice), and was a Clinton appointee to the federal appeals court (Rosemary Barkett); Barkett, incidentally, dissented from an 11th Circuit ruling denying a habeas petition to Troy Davis, the African-American death row inmate scheduled to be executed by the State of Georgia this week despite mountains of evidence showing his innocence.  So this episode highlights one of the few genuine differences that remain between the two parties that can truly impact people’s lives: their judicial appointments. 

But the overriding theme is what we have seen time and again, that which — as it turns out — is the subject of my book to be released next month: America is plagued by a two-tiered justice system in which political and financial elites enjoy virtually absolute immunity for even the most egregious of crimes, while ordinary Americans (and especially fully stigmatized ones like Padilla) are subject with few defenses to the world’s largest and one of its most merciless systems of punishment.  Thus do Jose Padilla’s lawless jailers and torturers walk free and prosper, while no punishment is sufficiently harsh for him. 

* * * * *
Almost immediately after I published this, it was announced that Troy Davis’ last chance for clemency has been denied, virtually assuring that a likely innocent man will be killed by the State of Georgia tomorrow.  Obviously, everything I just wrote applies in abundance to that event.

UPDATE:  As usual, America’s propaganda-spreading, government-serving establishment media spouts blatant falsehoods to justify all this; from ABC News:

From CNN:

Padilla was never even charged with, let alone convicted of, having anything to do with a “dirty bomb.”  “Dirty Bomber” was the villain nickname given to him by Bush officials and mindlessy repeated by its media to justify the treatment to which he was subjected.  The U.S. Government gave up long ago using this accusation to demonize him (NYT on his conviction: ”The dirty bomb accusations were not mentioned during Mr. Padilla’s three-month trial here“), but their lying “watchdog media” servants continue unabated.  Who would possibly object to a longer prison term for A Dirty Bomber who tried to detonate radioactive weapons in American cities?  The fact that not even the Government charged hi with that is no deterrent to its media continuing to claim he did.

UPDATE II:  Padilla was consigned to the SuperMax prison in Florence, Colorado to serve his 17-year sentence.  The New York City Bar Association last week issued a comprehensive study of America’s SuperMax system and concluded:

But 17 years in a torture system like that — on top of the 5 years of abuse he endured — is insufficient: ”too lenient.”