If it ever comes to court it should be one of the more interesting libel cases of the decade. The Iraqi National Intelligence Service is threatening to sue Ahmed Chalabi, the Iraqi politician, for asking who pays for it.

"It is somewhat curious," says Mr Chalabi, "that the intelligence service of a country which is sovereign – that no one really knows who is funding it."

In fact there are very few Iraqis who do not believe they have a very clear idea of who funds Iraq's secret police. Its director is General Mohammed Abdullah Shahwani, who once led a failed coup against Saddam Hussein, and was handpicked by the CIA to run the new security organisation soon after the invasion of 2003. He is believed to have been answering to them ever since.

The history of the Iraqi intelligence service is important because it shows the real distribution of power in Iraq rather than the spurious picture presented by President Bush. It explains why so many Iraqis are suspicious of the security accord, or Status of Forces Agreement, that the White House has been pushing the Iraqi prime minister Nouri al-Malki to sign. It reveals the real political landscape where President-elect Barack Obama will soon have to find his bearings.

For all Mr Bush's pious declarations about respecting Iraqi sovereignty, General Shahwani is reported to work primarily for American intelligence. The intelligence service is "not working for the Iraqi government – it's working for the CIA," Hadi al-Ameri, a powerful Shia lawmaker, was quoted as saying three years ago. "I prefer to call it the American Intelligence of Iraq, not the Iraqi Intelligence Service."

Mr Obama has a long-standing commitment to shut down Guantanamo, which has become a symbol of injustice for human rights campaigners, and a lightning rod for anti-US criticism since it opened eight years ago. Closing the prison, which is on a part of Cuba leased to the US, will bring to an end one of the most poisonous legacies of the Bush administration while sending a signal that the "war on terror" is under more enlightened management.

During his election campaign, Mr Obama described Guantanamo and the CIA's secret prisons around the world as a "sad chapter in American history". Other aspects of Mr Bush's "war on terror" will also demand Mr Obama's urgent attention such as the revelation by the New York Times that the US military has, during the past four years, conducted up to a dozen secret raids in Pakistan and other countries not at war with the US. Mr Obama has previously said he would approve such raids against enemies such as Osama bin Laden if there no other option was available.

Mr Obama's plans for Guantanamo inmates should see most detainees, against whom there is little or no evidence, being released to their home countries after years in legal limbo. Others will face prosecution in US criminal courts. One problem for those courts will face is deciding whether evidence from anonymous intelligence sources or obtained without any legal process can be taken into account. Some Guantanamo inmates suffered torture or other abusive treatment at the hands of CIA interrogators either at the prison or after they were picked up in security sweeps in Afghanistan or Pakistan. A few have been through the controversial military commissions process, from which even prosecutors have resigned. The US Supreme Court has several times rebuked the Bush administration for its handling of the detainees.