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:

In 2004, Gonzales was still President George W. Bush’s chief counsel. When Ashcroft did not give legal clearance for the then-secret National Security Agency surveillance program, the president held an “emergency meeting.”

At this meeting, the IG report says, Vice President Dick Cheney, then-NSA Director (now CIA Director) Michael Hayden and congressional leaders argued over the program’s lawfulness and whether it should continue. Gonzales took notes of the meeting– and then put them in a briefcase that he brought to his Vienna, Va., home.

The house, which Gonzales no longer lives in, had a safe. But Gonzales had forgotten its combination. A year later, when Gonzales became attorney general, he took the notes to his new Justice Dept. office. There, the documents were finally put in a safe — but not a “top secret” one, as legally required. Instead, they were stored where Justice Dept. employees could access them. Gonzales told the Justice IG this was OK, because he had written “AG-EYES ONLY-TOP SECRET” on the envelope that contained the notes.

The IG report also says Gonzales may have mishandled documents on detainee interrogation.

Meanwhile, the Justice Dept. has already said it won’t press charges against Gonzales.

The report doesn’t suggest Gonzales had any nefarious motive for not properly storing his notes. But, like the Justice’s politicized hiring report. it shows the former AG’s somewhat startling lack of professionalism.