BY JOSH MEYER

AND DAVID G. SAVAGE

Los Angeles Times

WASHINGTON - Attorney General Eric Holder's decision to prosecute the self-proclaimed architect of the Sept. 11 attacks and four others in a civilian, New York courthouse raised a raft of legal, political and ethical questions, including what kind of evidence will be used against men whom the U.S. government subjected to brutal interrogation methods.

In the case of plot mastermind Khalid Sheikh Mohammed, the CIA has acknowledged waterboarding, which many legal experts have said is torture.

"There could be all kinds of problems with the evidence. Some of it might be linked to waterboarding. Other evidence may have come from intelligence-gathering overseas," said Matthew Waxman, a Columbia University law professor who served as a top Pentagon lawyer in the Bush administration. "That said, the government would not be moving forward if they were not confident they can prove their case" with untainted evidence, Waxman said.

Lawyers for the five alleged 9/11 conspirators said they had no comment on how the men would plead once they are charged by federal prosecutors.

Holder said they would be prosecuted for the 2001 strikes. "They will be charged for what we believe they did," Holder said, "and that is to mastermind and carry out the 9/11 attacks."

[The New York Times reported in December 2008 that the detainees sought to plead guilty and be put to death in an act of martyrdom. But at the time, military judge Col. Stephen R. Henley said unanswered questions as to how military commissions dealt with capital cases needed to be resolved before the pleas could be accepted.

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[Among the issues to be considered, the Times said then, were uncertainty as to whether the death penalty could be imposed after a guilty plea rather than being found guilty by a panel of military officers. The defendants suggested then that they might withdraw their pleas if death wasn't assured.

[The Times also reported that lawyers representing two of the detainees suggested they might not be mentally competent enough to make such a plea. The others then declared they would withhold their pleas until the competency issue was resolved.]

Soon after taking office in January, President Obama directed Defense Secretary Robert Gates to ask prosecutors to seek stays for 120 days so terrorism cases at the facility could be reviewed.

Rep. Lamar Smith of Texas, the top Republican on the House Judiciary Committee, said holding the terrorism trials in civilian court could result in acquittals, mistrials or shorter sentences. He vowed that Republicans would redouble their recent efforts to block the proceedings through a congressional vote.

But Holder said he believed the suspects would be convicted based on evidence that would be allowed at trial - including "information that has not been publicly released."

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"I am confident," Holder said, "in the ability of our courts to provide these defendants a fair trial."