The Chilcot Inquiry into the Iraq war is a week old and even at this very early stage it appears that its chief victim could be Tony Blair, the man who has so successfully prevented the mud sticking to him hitherto. The questioning may have been gentle, but one after another, the top civil servants of the time have plunged the knife in to the former prime minister, sometimes brutally, sometimes with a surgeon's finesse. Whenever the question of responsibility for the war arose, they were clear that it was not theirs. Which is the constitutional truth. Their duty as civil servants is to execute the policies of the elected government, not, for all the fun and games of Yes, Minister, to thwart them.

Whether or not Tony Blair eventually emerges with the blame he has so long escaped, however, the inquiry is fast producing another candidate for chief loser. This one may be a bit more nebulous than the very distinct figure of our former prime minister. But if anything looks likely to come out of the Iraq inquiry even more sullied than Mr Blair's reputation, it is the "special relationship" between Britain and the United States. If this happens, the implications for British policy and Britain's image of itself would be profound.

Now some will argue that the "special relationship" was always a fiction, created and perpetuated by the British after the Second World War to cover the loss of empire. But it is difficult to deny that for decades there was genuinely something there. A fellow feeling, a shared sense of loyalty, all the assumptions now defined as "values" were bound up in it, even before you cite the exchange of intelligence so cherished by the relevant agencies.

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This relationship has, of course, had its ups and downs – including Harold Wilson's decision not to send troops to Vietnam, the US invasion of Grenada without Britain's say-so, and the policy – fronted by Washington's then ambassador to the UN, Jeane Kirkpatrick – to keep US links to Latin America open during the Falklands war.

But this little episode also illustrated the ambiguities of the "special relationship". Even as Ms Kirkpatrick and others strove to push Britain to negotiate with Argentina, the President and the Prime Minister – Ronald Reagan and Margaret Thatcher – were deep in their mutually admiring love-in. And what national leader other than Mrs Thatcher could have warned George Bush senior not to "go wobbly" after Iraq invaded Kuwait?

A generation on, the Iraq inquiry is showing, in merciless detail, how much has changed. What the early days of the Chilcot proceedings have exposed – far more than any misguided messianism on the part of Mr Blair, or any falling away of senior civil servants – is that the Reagan-Thatcher days are long gone, and that any attempt, by anyone, to see the Bush-Blair relationship in a similar light is a delusion.

This is not primarily a matter of personalities, though of both George Bush and Tony Blair it might be said respectively that they were no Ronald Reagan or Margaret Thatcher. The "special relationship", such as it was, could transcend personality. It is because the context by 2001, and particularly after 9/11, was quite different. The power and wealth relationship had been skewed many times over to the US advantage, while the ideological gap yawned as wide as the Atlantic.

The most striking story of the first days of the Chilcot Inquiry relates to the scale of the misunderstandings, disagreements and, above all, conflicts of interest and approaches that have been revealed between two countries that see themselves as close allies. Nor was this primarily a result of poor communication. Yesterday's witness, Mr Blair's foreign policy adviser, Sir David Manning, explicitly denied that there was any real difficulty in transatlantic communications. Both he and Mr Blair and Mr Blair's chief of staff appear to have had as much direct access to the White House and State Department as they could use.

The difficulty was that the United States and the British government, even under its abjectly pro-American Prime Minister, were actually saying very different things. Sir David Manning again: "For the US, regime change [in Iraq] could lead to disarmament; for the UK, disarmament could lead to regime change."

It fell to Sir Jeremy Greenstock, then our man at the UN, to try to conjure up a semblance of unanimity not only between the US and overtly reluctant warriors, such as France and Russia, but between the US and Britain as well. His skill in steering Resolution 1441 through the Security Council seemed a high point of his career at the time. But it could – as he now admits – also be seen as diplomacy "being too clever for its own good". There simply was no agreement, as became clear, to Britain's cost, when his efforts to force clarification on the use of force via the so-called Second Resolution failed.

The differences between Britain and the US – differences of principle, practice and perceived interests – look set to be further exposed. We have yet to hear about the destructive aftermath of the invasion, but when we do, all the evidence from recently leaked documents is that the quarrelling between the two capitals grew ever more acute.

Mr Blair may or may not have been as convinced of the need to remove Saddam Hussein by force as Mr Bush. But what he appears firmly to have believed is that it would be far more damaging to the world's peace and security if the US acted alone than if Britain stood alongside. This is the double conceit of the "special relationship"; first, that Britain's very presence might act as a restraint on the US, and second, that their interests are the same as ours.

We are now watching the selfsame illusion unravel in Afghanistan. British policy was stalled for months, waiting on the decision of another country's leader. Gordon Brown's Commons statement yesterday, like his subsequent video-conference with President Obama, were part of a charade designed to present as independent moves that were not independent at all.

The most productive result of the Iraq Inquiry might be to expose how the "special relationship" has had its day and now compromises our national interest. That might also be the people's ultimate revenge: to show Tony Blair how he destroyed what he loved the most.

m.dejevsky@independent.co.uk