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By Michael Isikoff National investigative correspondent
NBC News
updated 4/4/2011 7:28:39 PM ET 2011-04-04T23:28:39

Pentagon officials said Monday they will move rapidly to bring an entirely new war crimes case against Khalid Sheikh Mohammed and four other alleged  9/11 conspirators, aiming to formally present the charges against them in a military courtroom at Guantanamo Bay this year, according to administration officials and others familiar with the cases.

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But even administration officials conceded that the cases could drag on for years, with virtually every aspect bringing fresh legal challenges. “Basically, we’re in for the long haul,” said one administration official when asked how quickly a trial against the defendants can actually take place.

A basic problem is that the original military commission charges against Mohammed and his co-conspirators — brought in 2008 during the Bush administration — were formally withdrawn after Attorney General Eric Holder’s initial November 2009 decision to prosecute them in federal court in New York.

As a result, military prosecutors must now file a new set of charges and arraign the suspects, risking a potential replay of the circus-like proceeding three years ago at Camp Justice in Guantanamo, when Mohammed chanted holy verses in Arabic and declared his wish to become “a martyr.”

New law open to laundry list of legal challenges
The new attempt to bring the defendants to trial could prove just as problematic. Defense lawyers and other legal experts said the contents of a new military commissions law passed by Congress in 2009 provides fertile grounds for a host of new legal challenges on core issues, including the admissibility of key evidence and the right of the defendants to defense lawyers who are experts in death penalty law. 

“There will be years of litigation over the rules, the venue and the evidence before you get a final outcome,” said Anthony Romero, executive director of the American Civil Liberties, which has been helping to provide legal counsel to the defendants and which strongly criticized Monday's decision. 

Story: Professed 9/11 mastermind to be tried at Gitmo

That litigation will inevitably include allegations of torture and abuse  of some defendants, including Mohammed, who the CIA has acknowledged was waterboarded 183 times while in agency custody. There are also ongoing issues about whether two of the defendants are legally competent to stand trial, especially Ramzi bin al Shibh, whose lawyers have contended he was heavily drugged by military doctors in an effort to sedate him.

Holder, in reluctantly referring the case back to military commissions, conceded yet another problem when he told reporters at a press conference that it was “an open question” whether a defendant can plead guilty before a military commission (as Mohammed tried to do last time) and still receive the death penalty. Administration  officials noted Monday that there efforts under way in Congress to “fix” that problem by amending the military commissions law, but defense lawyers said such a change – like other elements of the case—could be challenged as an unconstitutional “bill of attainder.”

'Issues galore'
“If you wanted to have a quick and clear verdict, you wouldn’t refer this case to a military commission,” said one defense lawyer close to the case, who asked for anonymity. “There are issues galore that can keep this in the federal courts for years.”

Read more reporting by Michael Isikoff in the Isikoff Files

Capt. John Murphy, the chief prosecutor for the military commissions, said Monday that his office will swear new charges against the 9/11 defendants “in the near future.” While he did not give a time frame, another administration official told NBC News that there will be significant announcements of new military commission cases by early next week, one of them likely to be Abd Al Rahim Al Nashiri, the alleged mastermind of the bombing of the USS Cole in October 2000, who also was waterboarded.

The prospect that the 9/11 case could be met by seemingly endless delays and legal challenges came as some longtime supporters of the president criticized the move.

“I’m disappointed and surprised,” said Tom Malinowksi, the Washington director for Human Rights Watch and an informal adviser to White House officials. “I thought they were going to fight this.”

But a senior official who spoke on condition of anonymity said the administration had little choice once President Barack Obama, albeit reluctantly, decided in December to sign a defense bill that basically forbade the Pentagon from spending any money to fly the 9/11 suspects to the United States for any purpose. The White House basically decided then that “it wasn’t worth the fight” to continue to push for terror trials in federal courts in the face of stiff congressional resistance, leading directly to Holder’s announcement, the official said.

Another administration official said Holder was increasingly "focused" in recent months on the upcoming tenth anniversary of the 9/11 attack and the idea that the families of the victims needed to start seeing "justice."

© 2013 NBCNews.com  Reprints

Video: Trial for 9/11 attacks moved to Guantanamo

  1. Closed captioning of: Trial for 9/11 attacks moved to Guantanamo

    >>> in other news the obama administration pulled the plug on one of its signature efforts. it now says it's given up on a courtroom trial for the mastermind of the 9/11 attacks here inside the united states . instead khalid sheikh mohammed and others will be tried before military commissions at the base in guantanamo bay , cuba. pete williams has our report.

    >> reporter: a year and a half after announcing that the men accused of the 9/11 attacks would be on trial in new york attorney general eric holder said they will be tried at guantanamo.

    >> we simply cannot allow a trial to be delayed any longer for the victims of the 9/11 attacks or for their family members who have waited for nearly a decade for justice.

    >> reporter: that means no civilian courtroom for khalid sheikh mohammed , said to have been the mastermind, and four others accused of helping him. it's a turnaround for the obama administration after the president vowed on his first day in office to shut down gitmo within a year. new york 's mayor and police chief fought against bringing the terror trials there and congress rebelled blocking detainee moves to the u.s. in an interview with nbc the attorney general said he had no choice because congress put federal courts off limits.

    >> congress passed statutes that tie my hands.

    >> reporter: what of those who would say the attorney general should have seen this coming, that he could never sell the idea of these trials in the u.s.?

    >> it was always my belief that the american people , if they had an opportunity to look at these cases and hear both sides would have made the determination that the best thing is to go with the tried and true, to go with the system that has served us well and distinguishes us as a nation.

    >> reporter: republicans in congress today called it the right thing to do.

    >> the american people realized how wrong it was to hold a civilian trial in new york or in the continental united states .

    >> reporter: so did family members of the 9/11 victims.

    >> the man was caught in a military environment, in a war environment and should be tried in a military tribunal .

    >> reporter: tonight, military officials say they hope to have pretrial hearings under way in guantanamo by the 10th anniversary of the attacks this september with trials starting sometime later. brian?

    >> pete williams at the justice department tonight. pete, thanks. now

Timeline: Five 9/11 suspects to face military tribunals

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