The Supreme Court decision on Thursday on military commissions at Guantanamo Bay does more than raise questions about how the US will deal with the 450 prisoners at the prison. It may also have broader implications for how the Bush administration prosecutes the war on terror.

In 2002, President George W. Bush declared that members of al-Qaeda were not entitled to protections under the Geneva conventions. But the Supreme Court on Tuesday appears to have disagreed with that determination.