JIM LEHRER: Now Margaret Warner looks at what the Yemen terrorism connections mean for Guantanamo detainees.
MARGARET WARNER: Ever since taking office, President Obama has worked to honor his pledge to shut the prison at Guantanamo Bay, Cuba. But his January 2010 deadline has already slipped. Now the apparent connection between the suspect in the Christmas Day plot and an al-Qaida offshoot in Yemen has raised a new hurdle.
Nearly 100 Yemenis are still at Guantanamo, about half the total inmate population remaining there. Nearly half of those Yemenis have been cleared for release. But that was before yesterday's announcement from the president.
U.S. PRESIDENT BARACK OBAMA: Given the unsettled situation, I have spoken to the attorney general and we've agreed that we will not be transferring additional detainees back to Yemen at this time.
MARGARET WARNER: For retired U.S. Navy Commander Kirk Lippold, the decision came not a moment too soon.
COMMANDER KIRK LIPPOLD (RET.), U.S. Navy: I'm actually very pleased that the administration chose to do that. I think it shows that they recognize that the Yemeni government right now is having a very difficult time in maintaining control throughout the country.
MARGARET WARNER: Lippold was skipper of the USS Cole in October of 2000 when it was attacked by al-Qaida suicide bombers off the coast of Yemen. Seventeen American sailors were killed.
COMMANDER KIRK LIPPOLD: It would be unwise for us to return people back to that country, if in fact they have the potential to return back to al-Qaida and begin to fight on the battlefield.
MARGARET WARNER: In fact, only some 20 Yemenis have been released to date from Guantanamo. And Benjamin Wittes at the Brookings Institution in Washington says there's a reason for that.
BENJAMIN WITTES, Brookings Institution: The problem is, in short, that you have a group of people, a very large percentage of the total population of Guantanamo, many of whom are, from the U.S. government's point of view, pretty scary people, and a country that is very badly positioned to manage the risks that they pose in absorbing them.
MARGARET WARNER: And that, says Wittes, has meant that Yemenis have always been treated differently from others set for release at Guantanamo.
BENJAMIN WITTES: In addition to the scary Yemenis, there are a group of people there who, had they been Saudi, had they been from, you know, some other countries, would have gone home a long time ago.
MARGARET WARNER: Indeed, Yemen is a country of 22 million with a fragile government, facing secession in the south and rebellion in the north, not to mention crippling poverty.
It's proven fertile ground for al-Qaida in the Arabian Peninsula, the group claiming responsibility for the Christmas Day bombing attempt. Only one released Yemeni has returned to the battlefield, but many former Saudi Guantanamo detainees are now in al-Qaida's leadership there.
BENJAMIN WITTES: They went to Yemen for a reason. And the reason is that the long arm of the Saudi state and the long arm of any state has a lot more trouble reaching you in Yemen than it does in other places.
MARGARET WARNER: Washington attorney George Clarke represents two Yemenis at Guantanamo. He says decisions on who gets released should continue to be made on a case-by-case basis.
GEORGE CLARKE: I think both the Bush administration and the Obama administration tried to release people that they thought were not dangerous to the United States and -- or its interests. And I think that that analysis should continue into the future, as opposed to sort of some sort of blanket.
MARGARET WARNER: But, after what President Obama said Tuesday, Clarke says it isn't clear what happens next for one of his clients who had been slated for release.
GEORGE CLARKE: I don't -- I honestly don't know what happens to him. I mean, I think that's part of the problem. We know that there's a group of people who the Obama administration wants to move back to Yemen. And I think, with -- clearly, with this blanket prohibition, they're not going to be going anywhere for a while.
MARGARET WARNER: It's not just the fate of individual inmates that hangs in the balance. The president's temporary ban doesn't yet resolve larger politically charged questions that he and Congress have to wrestle with.
Republicans have argued the president was wrong from the start on Guantanamo. In a recent letter, Congressman Pete Hoekstra, ranking Republican on the House Intelligence Committee, said the Christmas Day incident requires Mr. Obama to abandon his -- quote -- "brazen and naive pledge to close Guantanamo Bay."
Hoekstra followed up Sunday on ABC's "This Week."
REP. PETE HOEKSTRA, R-Mich.: The core group of al-Qaida on the Arabian Peninsula is formed by former Gitmo detainees. These are people that were held in Gitmo, have been returned, and have now gone back to the battlefield.
MARGARET WARNER: Democratic Congresswoman Jane Harman, chairman of a House subcommittee on terrorism risk assessment, takes issue with that.
REP. JANE HARMAN, D-Calif.: It's way too simplistic. It is true that there was a connection between the Christmas Day bomber and Yemen. But Yemen is not the whole ball game. And I think that Guantanamo affords a recruiting tool that is unique worldwide to al-Qaida and other bad guys.
MARGARET WARNER: Harman does support the temporary freeze on repatriating Yemeni detainees, but says indefinitely holding them is not a permanent solution to this thorny problem.
One of the alternatives is to transfer the Yemeni prisoners, even those cleared for release, to a federal facility in Thomson, Illinois. The prison was chosen recently by the Obama administration to take detainees who are being prosecuted or can't be released elsewhere.
But that prospect remains murky, since it's unclear when or if Congress will fund the security upgrades needed at the prison.
REP. JANE HARMAN: I think the administration is sorting that out right now. This wrinkle about Yemen is fairly recent, and it is very serious. But we're going to have find -- they're going to have to find another answer.
MARGARET WARNER: Delay in finding an answer could pose another danger, warns Benjamin Wittes, that the courts could order the government to free those cleared for release in the U.S., if no other country will take them.
BENJAMIN WITTES: You could imagine a situation in which the government has a choice between Yemen and Cleveland. And that's, you know, a very unappealing choice from the government's point of view.
MARGARET WARNER: It could be a politically hazardous choice as well, given the passions already aroused by talk of releasing any Gitmo detainees anywhere here at home.