Under plans being put together in Obama's camp, some detainees would be released and many others would be prosecuted in U.S. criminal courts.
A third group of detainees - the ones whose cases are most entangled in highly classified information - might have to go before a new court designed especially to handle sensitive national security cases, according to advisers and Democrats involved in the talks. Advisers participating directly in the planning spoke on condition of anonymity because the plans aren't final.
The move would be a sharp deviation 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. Obama's Republican challenger, John McCain, had also pledged to close Guantanamo. But McCain opposed criminal trials, saying the Bush administration's tribunals should continue on U.S. soil.
The plan being developed by Obama's team has been championed by legal scholars from both political parties. But it is almost certain to face opposition from Republicans who oppose bringing terrorism suspects to the U.S. and from Democrats who oppose creating a new court system with fewer rights for detainees.
Laurence Tribe, a Harvard law professor and Obama legal adviser, said discussions about plans for Guantanamo had been "theoretical" before the election but would quickly become very focused because closing the prison is a top priority. Bringing the detainees to the United States will be controversial, he said, but 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 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.
"There would be concern about establishing a completely new system," said Rep. Adam Schiff, D-Calif., 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."
Obama has said the civilian and military court-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.
"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."
Though a hybrid court may be unpopular, other advisers and Democrats involved in the Guantanamo Bay discussions say Obama has few other options.
Prosecuting all detainees in federal courts raises a host of problems. Evidence gathered through military interrogation or from intelligence sources might be thrown out. Defendants would have the right to confront witnesses, meaning undercover CIA officers or terrorist turncoats might have to take the stand, jeopardizing their cover and revealing classified intelligence tactics.
In theory, Obama could try to transplant the Bush administration's military commission system from Guantanamo Bay to a U.S. prison. But Tribe said, and other advisers agreed, that was "a nonstarter." With lax evidence rules and intense secrecy, the military commissions have been criticized by human rights groups, defense attorneys and even some military prosecutors who quit the process in protest.
"I don't think we need to completely reinvent the wheel, but we need a better tribunal process that is more transparent," Schiff said.
That means something different would need to be done if detainees couldn't be released or prosecuted in traditional courts. Exactly what that something would look like remains unclear.
According to three advisers participating in the process, Obama is expected to propose a new court system, appointing a committee to decide how such a court would operate. Some detainees likely would be returned to the countries where they were first captured for further detention or rehabilitation. The rest could probably be prosecuted in U.S. criminal courts, one adviser said. All spoke on condition of anonymity to discuss the ongoing talks, which have been private.
Whatever form it takes, Tribe said he expects Obama to move quickly.
"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."