The secret order was signed months after the attacks. The New York Times says it authorized the National Security Agency to spy on Americans without a court order. The agency monitored international phone calls and Emails of thousands of Americans. Some NSA officials were reportedly so concerned about the legality of it all, they refused to participate.
The Patriot Act allows the FBI to go thru Americans’ bank, computer and library records. But a bipartisan group of senators is threatening a filibuster because they believe a compromise already agreed to gives the government too much power, and the president reversed course..
McCain's bill was designed to demonstrate that the mistreatment at Iraq’s Abu Ghraib prison and at secret CIA detention centers is not US policy. The McCain amendment says no prisoner in the custody of the US, "shall be subject to cruel, inhuman, or degrading treatment or punishment."
But the president and his advisers, led by Vice President Cheney, opposed it because among other reasons it did not give immunity to the CIA.
The new deal offers protection to any us agent including CIA officers who are following what they believe to be lawful orders.