Under the plan being drawn up by Obama's advisers, some detainees would be released and others would be charged in U.S. courts, where they would receive constitutional rights and open trials. But, underscoring the difficult decisions Obama must make to fulfill his pledge of shutting down Guantanamo, the plan could require creation of a new legal system to handle the classified information inherent in some of the most sensitive cases.
Many of the about 250 Guantanamo detainees are cleared for release, but the Bush administration has been unable to find a country willing to take them.
Advisers participating directly in the planning spoke on condition of anonymity because the plans are not final.
The plan being developed by Obama's team has been championed by legal scholars from both political parties. But as details surfaced Monday, it drew criticism from Democrats who oppose creating a new legal system and from Republicans who oppose bringing terror suspects to the U.S. mainland.
Obama foreign policy adviser Denis McDonough said the president-elect wants Guantanamo closed, but no decision has been made "about how and where to try the detainees, and there is no process in place to make that decision until his national security and legal teams are assembled."
Obama seeks a break from the Bush administration, which established military tribunals to prosecute detainees at the Navy base in Cuba and strongly opposes bringing prisoners to the United States. At the White House, spokeswoman Dana Perino said Monday that President George W. Bush has faced many challenges in trying to close the prison.
"We've tried very hard to explain to people how complicated it is. When you pick up people off the battlefield that have a terrorist background, it's not just so easy to let them go," Perino said. "These issues are complicated, and we have put forward a process that we think would work in order to put them on trial through military tribunals."
Obama has been critical of that process, and his legal advisers said finding an alternative would be a top priority. One of those advisers, Harvard law professor Laurence Tribe, acknowledges that bringing detainees to the United States would be controversial but said it could be accomplished.
"I think the answer is going to be, they can be as securely guarded on U.S. soil as anywhere else," Tribe said. "We can't put people in a dungeon forever without processing whether they deserve to be there."
"The Obama plan for the eventual closing of the detention facility at the military base - what we know of it, anyway - is a practical, reasonable solution to the problem the Bush administration created for itself in the aftermath of the terror attacks upon America," said.
"If done properly, with foresight and cooperation with the other branches, such a system would break the logjam over the rights of the terror detainees.
"This is no small matter. We are now more than seven years removed from September 11, 2001 and still there has been no completed military trial of a serious al Qaeda leader under tribunal rules initially set up by President Bush within months of the terror attacks."
The tougher challenge will be allaying fears by Democrats who believe the Bush administration's military commissions were a farce and dislike the idea of giving detainees anything less than the full constitutional rights normally enjoyed by everyone on U.S. soil.
"I think that creating a new alternative court system in response to the abject failure of Guantanamo would be a profound mistake," Jonathan Hafetz, an American Civil Liberties Union attorney who represents detainees, said Monday. "We do not need a new court system. The last eight years are a testament to the problems of trying to create new systems."
Senate Judiciary Committee member John Cornyn, a Republican, said it would be a "colossal mistake to treat terrorism as a mere crime."
"It would be a stunning disappointment if one of the new administration's first priorities is to give foreign terror suspects captured on the battlefield the same legal rights and protections as American citizens accused of crimes," Cornyn said Monday. He noted that the Senate overwhelmingly passed a nonbinding Senate bill last year opposing bringing detainees to the United States.
Obama did not vote on that measure. He has said the civilian and military courts-martial systems provide "a framework for dealing with the terrorists," and Tribe said the administration would look to those venues before creating a new legal system. But discussions of what a new system would look like have already started.
An Obama administration will want to avoid the criticisms that have marked the Bush administration's military commissions. Human rights groups and defense attorneys have condemned the commissions for lax evidence rules and intense secrecy. Some military prosecutors have even quit in protest.
"It would have to be some sort of hybrid that involves military commissions that actually administer justice rather than just serve as kangaroo courts," Tribe said. "It will have to both be and appear to be fundamentally fair in light of the circumstances. I think people are going to give an Obama administration the benefit of the doubt in that regard."
Some were not so sure.
"There would be concern about establishing a completely new system," said Democratic Rep. Adam Schiff, a member of the House Judiciary Committee and former federal prosecutor who is aware of the discussions in the Obama camp. "And in the sense that establishing a regimen of detention that includes American citizens and foreign nationals that takes place on U.S. soil and departs from the criminal justice system - trying to establish that would be very difficult."
Although a hybrid court might be unpopular, other advisers and Democrats involved in the Guantanamo Bay discussions say Obama has few options.
Prosecuting all detainees in federal courts raises many problems. Evidence gathered through military interrogation or from intelligence sources might be thrown out. Defendants would have the right to confront witnesses; that means undercover CIA officers or terrorist turncoats might have to take the stand, jeopardize their covers and reveal classified intelligence tactics.
That means something different would need to be done if detainees could not be released or prosecuted in traditional courts. Exactly what remains unclear.
"I don't think we need to completely reinvent the wheel, but we need a better tribunal process that is more transparent," Schiff said.
According to three advisers participating in the process, Obama is expected to propose a new court system and may appoint a committee to decide how such a court would operate. Some detainees probably would be returned to the countries where they were captured for further detention or rehabilitation. The rest probably could be prosecuted in U.S. criminal courts, one adviser said. All spoke on condition of anonymity to discuss the continuing talks, which have been private.
One challenge will be to figure out what to do with the 90 or so Yemeni detainees, the largest group in the prison. The Bush administration has sought to negotiate the release of some of those detainees as part of a rehabilitation plan with the Yemeni government. Talks have so far been fruitless.
Waleed Alshahari, who has been following Guantanamo issues for the Yemeni Embassy in Washington, said the plan being discussed by the Obama team was an improvement over the current system. But he said he expects most detainees to be released rather than stand trial.
"If the U.S. government has any evidence against them, they would try them and put them in jail," Alshahari said. "But it has been obvious they have nothing against them. That is why they have not faced trial."
Whatever Obama decides, he should move quickly, Tribe said.
"In reality and symbolically, the idea that we have people in legal black holes is an extremely serious black mark," Tribe said. "It has to be dealt with."