The arguments made in the Ghailani case are a good indication of the kinds of claims that the suspected co-conspirators of the 9/11 terrorist attacks may make when their case begins in the same federal courthouse next year. The government’s response in this case similarly reveals how it’s likely to oppose any moves to dismiss the 9/11 cases.

The government’s argument in the Ghailani case can be summed up as: 1) it’s Ghailani’s own fault for being a fugitive before Sept. 11, 2001, while his co-conspirators all got prompt trials in New York; and 2) after the 9/11 terrorist attacks, the need for intelligence trumped all, and the speedy trial requirement got thrown out the window.

The way the government explains is it is somewhat more artful. After 9/11, the United States was at war. So Ghailani, who’d previously been charged as a civilian criminal along with other suspects, who were tried and convicted earlier in 2001, was suddenly transformed into a war criminal. And that changed all of the rules.

Given the threat of another major terrorist attack after 9/11, “the Government had shifted dramatically toward intelligence-gathering as the primary means to prevent such an attack.” When Ghailani was captured in 2004, “the defendant was believed to have, and in fact did have, actionable intelligence about al Qaeda — by virtue of his longstanding position in al Qaeda, his assistance to known al Qaeda terrorists” and his alleged ongoing relationship with Osama bin Laden.

Of course, none of these relationships had actually been proven by the time the government captured Ghailani, since he hadn’t had any sort of trial. But the government’s argument is that because he was believed to have information about al-Qaeda, it was justified in detaining him in a CIA prison, and then at the prison camp at Guantanamo Bay for another five years.

“In light of these extraordinary circumstances, the Government justifiably opted to initially treat the defendant as an intelligence asset,” the government writes.

The details of Ghailani’s imprisonment and interrogation by the CIA are all redacted in the government’s brief. But in the brief asking the court to dismiss the case, Ghailani’s lawyers argue that he was physically and psychologically abused during two years of overseas CIA imprisonment and interrogations at places where techniques “amounting to torture” had been authorized. Ghailani was also denied the right to a lawyer.

Ghailani was eventually charged in 2008 by the military commissions, but that proceeding was stalled after President Obama took office. Ghailani’s case was transferred to a civilian federal court in May.

“We respectfully submit that this case presents possibly the most unique and egregious example of a speedy trial violation in American jurisprudence to date,” Ghailani’s lawyers wrote in their brief.

The right to a speedy trial derives from the Sixth Amendment to the U.S. Constitution. The Supreme Court, however, said in a 1972 case that judges should weigh several factors in deciding whether the right had been violated, including the length of the delay and its reason, whether the defendant himself was to blame, and whether the delay would prejudice the defendant’s case.

Ghailani’s lawyers have said that their client “appears to be so damaged” by his treatment in U.S. that he may be unable to help his lawyers prepare his defense. They’ve asked the court to have an expert examine the mental state of their client.

Here is the Justice Department’s brief:

Ahmed Ghailani, a Tanzanian seized in Pakistan in 2004 suspected of participation in the 1998 US embassy bombings in East Africa, spent two years under interrogation in a secret CIA prison before being sent to Guantanamo in 2006.

Given that he’d already been indicted in federal court for the 1998 charges, though, the Obama administration decided to just try him there, where it apparently believes he should have been tried all along. After all, he’s not charged with having anything to do with the 9-11 attacks, which is what the prison at Guantanamo Bay was supposedly set up to deal with.

To reinforce the point that the federal court system is perfectly capable of handling Ghailani’s case, the Justice Department today has sent out this fact sheet listing some of the major international terror cases that have been tried in the Southern District of New York, including the 1993 World Trade Center bombing, which led to the conviction and life sentences of six plotters.

The fact sheet also notes that there are now 216 inmates in federal prisons with connection to international terrorism — and surprisingly, none have escaped and rampaged in their local federal prison communities.

Of course, this all raises the question: if the government is so proud of its record prosecuting international terrorists, then why doesn’t it just transfer all the Gitmo prisoners it has evidence against and charge them in U.S. federal courts?

Why is the administration still intent on creating new military commissions, and even holding some suspects indefinitely without trial?

Coincidentally, the Senate Judiciary Committee today is addressing the question of indefinite detention at a hearing entitled, “The Legal, Moral, and National Security Consequences of Prolonged Detention.”

The Obama administration is now apparently trying to fix the mess that its predecessor created, at least in this case, but it’s got a problem: can it now try a defendant arrested five years ago for a crime committed in 1998? Just last week, a lawyer for Ghailani told a federal judge that he would seek dismissal of his client’s indictment because the government has violated his right to a speedy trial under U.S. law, and blocked the lawyer from even communicating with his client since July 2008.

In 2007, Mr. Ghailani reportedly apologized before a military review panel at Guantánamo for his role in assisting the embassy bombing, which he says he didn’t know about. “It was without my knowledge what they were doing, but I helped them,” he said, according to a transcript obtained by The New York Times. He added, “I’m sorry for what happened to those families who lost, who lost their friends and their beloved ones.”