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Charges bring the "trial of the century" one step closer.
The Defense Department issued a statement saying that terrorist ringleader Khalid Sheikh Mohammed and the four others accused "could be sentenced to death" if found guilty of plotting the attacks in New York, Washington, and Pennsylvania that killed a total of 2,976 people.
The five are charged with "terrorism, hijacking aircraft, conspiracy, murder in violation of the law of war, attacking civilians, attacking civilian objects, intentionally causing serious bodily injury, and destruction of property in violation of the law of war," said the statement.
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The group was initially charged by the Bush administration in June 2011, said the BBC, but there were delays due to disputes over whether they would face a military tribunal, which is closed to the public, or face a jury-based civil court trial.
The Obama administration first advocated for a trial in civilian courts, a move that saw widespread resistance in the United States. The government reversed its stance in April 2011, according to BBC.
They are due to appear before a military court at the US naval base Guantanamo Bay, Cuba, within 30 days for preliminary proceedings, said the Defense Department.