US Defence Secretary Lloyd Austin on Friday overrode a plea agreement reached earlier this week for the accused mastermind of the September 11, 2001, attacks and two other defendants, reinstating them as death penalty cases.
The move comes two days after the military commission at Guantanamo Bay, Cuba, announced it had reached plea deals with Khalid Sheikh Mohammed and two accused accomplices, Walid bin Attash and Mustafa al-Hawsawi, in the attacks.
Letters sent to families of the nearly 3000 people killed in the al-Qaida attacks said the plea agreement stipulated the three would serve life sentences.
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Some families of the attack's victims condemned the deal for cutting off any possibility of full trials and possible death penalties.
Republicans were quick to fault the Biden administration for the deal, although the White House said after it was announced it had no knowledge of it.
Austin wrote in an order released Friday night that "in light of the significance of the decision," he had decided that the authority to make a decision on accepting the plea agreements was his.
He nullified the agreements.
Mohammed and the other defendants had been expected to formally enter their pleas under the deal as soon as next week.
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The US military commission overseeing the cases of five defendants in the September 11 attacks has been stuck in pre-trial hearings and other preliminary court action since 2008.
The torture that the defendants underwent while in CIA custody has slowed the cases and left the prospect of full trials and verdicts still uncertain, in part because of the inadmissibility of evidence linked to the torture.
Lawyers for the two sides have been exploring a negotiated resolution to the case for about 1.5 years.
President Joe Biden blocked an earlier proposed plea bargain in the case last year, when he refused to offer requested presidential guarantees that the men would be spared solitary confinement and provided trauma care for the torture they underwent while in CIA custody.
A fourth September 11 defendant at Guantanamo had been still negotiating on a possible plea agreement.
The military commission last year ruled the fifth defendant mentally unfit to stand trial.
A military medical panel cited post-traumatic stress disorder and psychosis, and linked it to torture and solitary confinement in four years in CIA custody before transfer to Guantanamo.