The result of a hearing Monday in the case of al Qaeda confederate Ahmed Khalfan Ghailani, who is accused of helping to blow up two U.S. embassies in Africa, could have far-reaching implications for the federal government’s decision to try the alleged 9/11 terrorists in the civilian justice system in New York.

Judge Lewis A. Kaplan will hear arguments Monday on whether or not the indictment against Mr. Ghailani in United States v. Hage, 98 cr. 1023 (S-10), should be dismissed on speedy trial grounds, a decision that could serve as a template for the pretrial maneuvering in the controversial case against Khalid Sheikh Mohammed and four others for the Sept. 11, 2001, hijacking of four airliners and attacking New York City and Washington.

Read the indictment, the defense’s speedy-trial motion and the government’s response.

Mr. Ghailani’s attorneys say their client’s case is unique in one respect—he was arrested in Pakistan in 2004 and then detained and interrogated at CIA “black sites” before being sent to the Guantánamo Bay detention facility on Sept. 6, 2006, for trial by military commission, almost eight years after he had already been indicted in the Southern District for the Aug. 7, 1998, bombings of the U.S. embassies in Dar es Salaam, Tanzania, and Nairobi, Kenya, that killed 224 people.

On the surface, the precedent for Mr. Ghailani’s trial would seem to be the 2001 convictions of four co-defendants in the Southern District in the same crimes.

But there is a critical difference between the two cases. The four men who were convicted in the embassy bombings were quickly arrested and brought to New York for trial before Judge Leonard Sand. By contrast, Mr. Ghailani’s capture came in a post-9/11 world, a point the prosecutors strongly emphasize in their December briefs opposing a speedy-trial dismissal of the charges against Mr. Ghailani.

“Unlike his co-defendants who were previously tried in this case, the defendant, a foreign national, was captured abroad after spending six years as a fugitive from justice; while working directly with top al Qaeda terrorists; as the United States was waging a difficult war against al Qaeda; and following a terrorist attack by al Qaeda on American soil that left almost 3,000 Americans dead,” prosecutors from the Southern District U.S. Attorney’s Office say in their briefs.

Mr. Ghailani, they argue, was “captured during a war,” when “the government had shifted dramatically toward intelligence-gathering as the primary means to prevent such an attack,” and so the United States “justifiably opted to initially treat the defendant as an intelligence asset,” and hold him as an enemy combatant.

“This was done, simply put, to save lives,” said the prosecutors, who will likely make the same argument when Mr. Mohammed and his 9/11 co-defendants arrive in New York for trial.

But it is what happened during the time Mr. Ghailani was held as an enemy combatant that defense lawyers argue justifies dismissing the indictment on speedy-trial grounds, according to their memo filed in November.

Mr. Ghailani’s attorneys, Gregory E. Cooper and Michael K. Bachrach, both solo practitioners, and Peter Enrique Quijano of Quijano & Ennis, claim that once Mr. Ghailani was arrested during a gun battle with Pakistani authorities on July 24, 2004, and transferred to the CIA’s secret prisons, he was subjected to enhanced interrogation techniques. The lawyers in their memo describe their client’s treatment as “systematic physical and psychological abuse” in violation of the Universal Declaration of Human Rights and the Geneva Convention.

The defense lawyers also claim the government cannot get away with the delay because of the CIA’s effort to turn Mr. Ghailani, 38, into an intelligence asset, a move the defense characterized as “a political decision with consequences.”

Rationale for Delay

The government’s December memo in opposition makes several arguments that were blacked out as top secret. But in the visible part of the memo, the prosecutors argue that “the existence of other proceedings” was another valid reason for the delay, that Mr. Ghailani failed to demand a speedy trial, and that he was not prejudiced by the delay.

The government can be expected to make similar arguments should Mr. Mohammed and his co-defendants seek speedy-trial dismissal on the basis of mistreatment during interrogations.

But Mr. Mohammed and his fellow Guantánamo detainees are not likely to arrive in New York any time soon. The executive branch must first issue a report to Congress on the proposed criminal trial. Once Congress receives that report, the earliest the men could be transferred is 45 days later.

The announcement that the 9/11 defendants would be tried in lower Manhattan prompted a wave of criticism, specifically, that the trials would encourage further terrorist attacks on New York City, would confer rights to terrorists who would use the trial as a propaganda platform, and would hurt national security because mandated disclosures to the defense would compromise intelligence sources and methods.

For this reason, the pretrial proceedings in the Ghailani case are being watched closely.

Mr. Cooper said he cannot say much about the case, but in a recent interview he observed that the speedy-trial issues and problems with discovery and security in the Ghailani case will influence and presage developments in the Mohammed trial.

Mr. Cooper pointed to a strict protective order signed by Judge Kaplan in July pursuant to the Classified Information Procedures Act.

The protective order in the case of Khalid Sheikh Mohammed “will probably be similar to ours: the limitations placed on us will certainly provide guidelines,” Mr. Cooper said. “I didn’t think we were the leaders, but there are certain things we are first on.”

The defense lawyers themselves had to obtain security clearances to see classified information and then sign a memorandum of understanding to abide by special administrative measures imposed by the Bureau of Prisons that prevent the passing of information to Mr. Ghailani.

‘Dancing in the Dark’

Motions in the Ghailani case are filed under seal and screened by a designated court security officer and are only released after sensitive information is redacted.

Mr. Cooper said the process is arduous and makes it hard to prepare a defense.

“The limitations on what the public can know and the limitations on what the defendant can know are probably equal,” Mr. Cooper said. “It’s tough to represent someone when you are dancing in the dark. The limitations on the disclosure of information are unfair. Any lawyer will tell you that if you are limited in what you can discuss and how you can discuss it, it’s hard to represent a client.”

The difficulty of even determining what can be discussed in open court was demonstrated during arguments over discovery, including the run-up to the speedy-trial motion, as the defense attempted to learn the location of the black sites and the amount of time Mr. Ghailani was held at each one. His attorneys asked prosecutors to search for and turn over memos from high-ranking White House and U.S. Department of Justice officials on the decisions to move and interrogate Mr. Ghailani during his years in custody.

‘Duty to Search’

Judge Kaplan this week ordered the unsealing of transcripts of three meetings he held with the defense and prosecution teams on Nov. 5, Nov. 18 and Dec. 9, 2009.

On Nov. 5, the transcript shows, Mr. Bachrach asked for any White House and U.S. attorney general memos on “several key decisions,” specifically the decisions to send Mr. Ghailani somewhere other than the Southern District in 2004, to transfer him to Guantánamo, to charge him militarily and then, finally, to send him to New York last year.

Southern District Assistant U.S. Attorney Michael Farbiarz’s response at the hearing addressed some of the factors the U.S. Supreme Court said should be considered in speedy-trial motions—the reasons for delay and the motives of the government. Barker v. Wingo, 407 U.S. 514 (1972).

“We have looked and looked and looked and we have not seen…evidence that begins to suggest that the decision to place Mr. Ghailani in an interrogation program or to transfer him to Guantánamo even begins to be part of a desire to punish him, a fit of spite [or] anything like that,” Mr. Farbiarz said.

But he also said, “It is hard for us to understand why our duty to search extends to presidential communications and such.”

Judge Kaplan, saying he was playing “devil’s advocate,” asked Mr. Farbiarz, “Why isn’t the background of the reasons for each one of these decisions, including who made the calls on the basis of what information and with what objectives in mind, relevant to the prong in Barker v. Wingo that requires me to consider the reason for the delay?”

Mr. Farbiarz said he could see having a duty to search further for relevant memos or communications where there was “some indication that the subjective motives were bad,” but, here, he said, there were no such indications.

“Define ‘bad,’” Judge Kaplan said.

“A desire to punish, rather than a desire to interrogate,” Mr. Farbiarz said, adding later, “We just haven’t seen anything that says, ‘Oh, gee, we don’t like this guy, he is a terrorist. Let’s do something bad to him.’”

Also on Nov. 5, Mr. Bachrach complained that, in a prior ex parte meeting with Judge Kaplan, prosecutors cited oral rulings of other judges from the bench in Classified Information Procedures Act cases.

To the extent the government relies on those rulings, Mr. Bachrach said he is “at a great disadvantage. There is no classified Westlaw.”

Despite reassurances from Mr. Farbiarz that the information would be shared, Mr. Bachrach said, “It creates an incredibly uneven playing field, in our opinion.”

The issue of document sharing has since been resolved.

According to the transcript of the Nov. 18 hearing, one issue for discussion was the defense’s desire to hire a “contractor,” a term that was not defined, to review classified information and discuss with Mr. Ghailani “a variety of subjects, including interrogation techniques that were applied to him.”

One concern for the defense was how to have the “contractor” sign the memorandum of understanding on the protective order and sign an affidavit promising to abide by the special administrative measures, without the prosecution team learning his or her identity.

At the Dec. 9 hearing, in the part of the session held in open court on the breadth of the government’s obligation to produce discovery in the case, Judge Kaplan said there was one difficulty: the parties were going to have to proceed without the benefit of the papers, because they were still being reviewed for classified information.

“But that’s simply inevitable, given the nature of the case and the nature of some of the evidence,” the judge said.

Once the attorneys began to approach the line where they would, of necessity, talk about classified material, the session would be closed to the public, the judge said.

In addition to Mr. Farbiarz, the memo was submitted by Assistant U.S. Attorneys Jesse M. Furman, Harry A. Chernoff, Nicholas Lewin and Sean S. Buckley.