Connell’s client, Baluchi, allegedly assisted some of the hijackers with travel arrangements and money transfers. Connell contends that the case against his client “is much weaker without a conspiracy count. The allegations against Mr. al Baluchi is that he was a logistical supporter at most.”

He also decried MacDonald’s decision to keep the conspiracy charge, over the wishes of the chief prosecutor. MacDonald’s title is “convening authority,” a role that’s uniquely military in that it gives a senior official oversight of a prosecution.

“The Convening Authority’s decision to require a charge to go forward when the Chief Prosecutor says that it is not legally viable demonstrates that the Convening Authority is in no way a neutral body,” said Connell. “The Convening Authority’s attempt to drive the prosecution forward shows that the military commission structure is fundamentally unfair.”

The current Sept. 11 hearings set the conditions for the trial, more than a year away, before a jury of U.S. military officers.

In a separate ruling, Pohl refused to decide a fundamental legal question looming over the case — how many protections of the U.S. Constitution the Guantánamo defendants get.

Defense lawyers asked the judge to rule that the Constitution is presumed to apply, unless the prosecution succeeds in court in stripping away certain rights. Pohl wrote that the lawyers were seeking an “advisory opinion,” and then noted, as he has said repeatedly in court, that he doesn’t issue those. Instead, he said, he would only rule on a specific question, as it comes up in the case.

Prosecutors have argued that the Constitution does not broadly apply at the war court, and that the U.S. Supreme Court has only granted Guantánamo detainees the right to have a civilian court review their detention.