IN The Good Shepherd, Robert De Niro's forthcoming film about the birth of the CIA, there are several chilling moments. One of the iciest occurs as the Virginia farmboys are moving into their new headquarters at Langley. From the marbled halls and sheer size of the place it is plain this is a home built for emperors. One of the agents says a politician asked him why the organisation always referred to itself as "CIA" and never "the CIA". His answer: "You don't put a the' in front of God, do you?"

This week, the unthinkable happened to the untouchables. German prosecutors issued arrest warrants for 13 CIA agents in connection with the alleged abduction of a German citizen. Khaled al-Masri says he was kidnapped in Macedonia in 2003, taken to Afghanistan and accused of having ties to al Qaeda. After five months of interrogation, during which he claims to have been beaten, his captors realised they had lifted the wrong man and dumped him in Albania.

The German warrants are not the first. Italian prosecutors want to charge 25 CIA agents over the "extraordinary rendition", as the process of snatch and despatch to secret prisons is known, of a cleric from Milan. The German charges are more significant because of the country's strategic importance to the US, and the weight of evidence al-Masri, with the help of his lawyer and journalists, has been able to amass.

From being a lone voice telling a strange tale that few believed, al-Masri has the attention of the German public, media, parliament and prosecutors. Questions are being asked of ministers.

In reality, the odds on 13 CIA agents standing in a German dock this time next year are on a par with Dick Cheney becoming head of Amnesty International. The agents, naturally, operated under aliases. The only body that could reveal their true identities, or hand them over, is the US government. Since that would involve breaking its own law, the Intelligence Agencies Protection Act, and exposing the workings of the CIA to the full glare of day, it's not going to happen.

The fact that the courts in Germany and Italy should even try to call CIA agents before them is what matters. There was no such disrespect shown in the agency's early years, abroad or at home. The CIA was there to fight the good fight against communism, and was left to get on with the job, no questions asked, every budget approved. The Bay of Pigs, Watergate and exposure of the agency's workings, including the assassination of foreign leaders, followed. By the millennium, the CIA had been effectively fenced in by Congress. Then came September 11. Instead of punishing the CIA for failing to prevent the greatest peacetime attack on mainland America, the president, whose father, remember, had once headed the agency, restored the carte blanche it had enjoyed in the fifties.

Under the president's guidance, the CIA has not used its regained freedom well. The first rule of espionage is to blend in. Adapt to the environment. Work with it. The CIA is acting like an 800lb gorilla let loose in a production of Swan Lake.

For a so-called secret policy, extraordinary rendition is attracting an astonishing amount of attention. This is no longer about crowds protesting outside airports, as they did in Scotland; it's court wrangles and diplomatic incidents. It's the kind of heat no intelligence agency wants to attract, because it involves those lethal weapons known as judiciaries and governments with reputations to protect. Particularly now, when America's standing abroad is so low, no democratically-elected government, save the one led by Tony Blair, is going to take the CIA's side against its own citizens. Those citizens, meanwhile, are more powerful than they've ever been. They're better informed, more sceptical, less deferential. They constitute an intelligence organisation of their own.

The CIA faces a choice. It can continue crashing into the local scenery or adapt to suit the rapidly changing environment. Extraordinary rendition is the stuff of the early Cold War transferred to the 21st century. It's an offence against morality, reason, and as prosecutors in Germany and Italy have decreed, against the law, too.

Over in Langley they're not likely to be losing much sleep over court decisions in far-away lands. The gods don't concern themselves too much with little people. Yet the multi-billion budget CIA should be asking itself how an unemployed man from Germany has been able to take his claims this far. The next man, the next government, might get further. By then, there will be someone else in the White House, someone who realises one of the most significant battles in any war - terror or otherwise - is the one for hearts and minds. Are the farmboys up to that fight?