Donald Rumsfeld, the defence secretary, explained that Boykin was exercising his rights as a citizen: "We're a free people." President Bush declared that Boykin "doesn't reflect my point of view or the point of view of this administration". Bush's commission on public diplomacy had reported that in nine Muslim countries, just 12% believed that "Americans respect Arab/Islamic values". The Pentagon announced that its inspector general would investigate Boykin, though he has yet to report.

Boykin was not removed or transferred. At that moment, he was at the heart of a secret operation to "Gitmoize" (Guantánamo is known in the US as Gitmo) the Abu Ghraib prison. He had flown to Guantánamo, where he met Major General Geoffrey Miller, in charge of Camp X-Ray. Boykin ordered Miller to fly to Iraq and extend X-Ray methods to the prison system there, on Rumsfeld's orders.

Boykin was recommended to his position by his record in the elite Delta forces: he was a commander in the failed effort to rescue US hostages in Iran, had tracked drug lord Pablo Escobar in Colombia, had advised the gas attack on barricaded cultists at Waco, Texas, and had lost 18 men in Somalia trying to capture a warlord in the notorious Black Hawk Down fiasco of 1993.

Boykin told an evangelical gathering last year how this fostered his spiritual crisis. "There is no God," he said. "If there was a God, he would have been here to protect my soldiers." But he was thunderstruck by the insight that his battle with the warlord was between good and evil, between the true God and the false one. "I knew that my God was bigger than his. I knew that my God was a real God and his was an idol."

Boykin was the action hero side of his boss, Stephen Cambone, a conservative defence intellectual appointed to the new post of undersecretary of intelligence. Cambone is universally despised by the officer corps for his arrogant, abrasive and dictatorial style and regarded as the personal symbol of Rumsfeldism. A former senior Pentagon official told me of a conversation with a three-star general, who remarked: "If we were being overrun by the enemy and I had only one bullet left, I'd use it on Cambone."

Cambone set about cutting the CIA and the state department out of the war on terror, but he had no knowledge of special ops. For this the rarefied civilian relied on the gruff soldier - a melding of "ignorance and recklessness", as a military intelligence source told me.

Just before Boykin was put in charge of the hunt for Osama bin Laden and then inserted into Iraqi prison reform, he was a circuit rider for the religious right. He allied himself with a small group called the Faith Force Multiplier that advocates applying military principles to evangelism. Its manifesto - Warrior Message - summons "warriors in this spiritual war for souls of this nation and the world ... "

Boykin staged a travelling slide show around the country where he displayed pictures of Bin Laden and Saddam Hussein. "Satan wants to destroy this nation, he wants to destroy us as a nation, and he wants to destroy us as a Christian army," he preached. They "will only be defeated if we come against them in the name of Jesus". It was the reporting of his remarks at a revival meeting in Oregon that made them a subject of brief controversy.

There can be little doubt that he envisages the global war on terror as a crusade. With the Geneva conventions apparently suspended, international law is supplanted by biblical law. Boykin is in God's chain of command. President Bush, he told an Oregon congregation last June, is "a man who prays in the Oval Office". And the president, too, is on a divine mission. "George Bush was not elected by a majority of the voters in the US. He was appointed by God."

Boykin is not unique in his belief that Bush is God's anointed against evildoers. Before his 2000 campaign, Bush confided to a leader of the religious right: "I feel like God wants me to run for president ... I sense my country is going to need me. Something is going to happen."

Michael Gerson, Bush's chief speechwriter, tells colleagues that on September 20 2001, after Bush delivered his speech to the Congress declaring a war on terror, he called Gerson to thank him for writing it. "God wants you here," Gerson says he told the president. And he says that Bush replied: "God wants us here."

But it's Bush who wants Rumsfeld, Cambone and Boykin here.

· Sidney Blumenthal, a former senior advisor to President Clinton, is Washington bureau chief of Salon.com

Sidney_Blumenthal@yahoo.com