• US wants UK to stay in EU but is opposed to independent Scotland • SNP wants an independent Scotland to be in EU • UKIP wants UK (including Scotland) out of EU

During a recent discussion about the prospect of Scottish independence, a senior British defence official interjected: "The Americans will be furious".

What was significant about the remark was not that the US was opposed to an independent Scotland. They like stability in their close allies and, after all, Britain's lone Trident missile fleet is based in Scotland and the SNP is opposed to nuclear weapons.Washington does not want anyone to upset the status quo, certainly nothing which raises questions about the future of the UK's nuclear arsenal.

What is significant is that the Whitehall establishment treats the US as an arbiter of what is in Britain's interests and, indeed, of how Britons – or, in this case, people living in Scotland, should vote.

Defence chiefs adopt a nonchalant air when it comes to the Scottish referendum, claiming that they have not bothered to draw up a contingency plan in the event of a Yes vote. If true, this would be very strange since, as I have mentioned before, the Ministry of Defence has a contingency plan for every possible eventuality, including an American invasion of the UK.

Actually, given the importance Whitehall, and most of Westminster, seems to attach to Britain's Trident nuclear missile fleet, an arrangement could be reached, at least in the short or even medium term, on the Faslane and Coulport bases.

(A report released on Wednesday by the British thinktank, Chatham House, argues that the Scottish vote on independence will have major consequences for the defence and national security of Scotland and the United Kingdom, whatever the outcome. It adds that a No vote would not end the matter or represent a return to the status quo. "The continuing basing of the United Kingdom's nuclear deterrent in Scotland will inevitably be revisited, with the future of the bases at Faslane and Coulport open to question. There may also be a questioning of the closure of the Portsmouth shipyard and the concentration of the surface ship building on the Clyde", says professor Andrew Dorman.)

Nuclear weapons are just one, and not even the most important, aspect of the "special relationship", an unequal relationship which, as far as Whitehall is concerned, is essentially based on money. It is valuable because it so "useful", as another senior British defence official told me.

We get the Trident missiles at a "special" price from the US, the missiles are serviced in the US, and US technology and know-how helps in the design and modernisation of warheads at the Atomic Weapons Research Establishment at Aldermaston. The 1958 UK-US mutual defence agreement, due to be renewed this year, is a traditional pillar of the "special relationship". Its contents are classified.

Britain has a unique intelligence relationship with the US, one, as we have recently seen, that encourages British security and intelligence agencies collude in CIA torture and NSA surveillance. The NSA helps pay for GCHQ listening posts. In return, GCHQ, as a 1994 staff manual put it, applies UK resources "to the meeting of US requirements".

Britain's close ties with the US is the subject of a newly published book, America and Britain, Was There Ever a Special Relationship? (by Guy Arnold, published by Hurst).

The occasions when Britain did not do America's bidding are few. One, often cited, is Harold Wilson's Labour government declining to deploy British troops to Vietnam – though Britain supplied more discreet support in the form of intelligence, special forces, and MI6 stations in Hanoi and Hong Kong.

More noticeable was Edward Heath's refusal, noted by Arnold, during the 1973 Yom Kippur War to allow US intelligence-gathering from British bases in Cyprus – and his decision to place an arms embargo on all sides thereby preventing Israel obtaining spare parts for its Centurion tanks.

Surveillance, Secrecy, and Sovereignty, by Margaret Nunnerley (Burley Publications), describes how the Campaign for the Accountability of American Bases has shed light on the activities of US intelligence agencies in Britain, notably the NSA's large – and growing – eavesdropping base at Menwith Hill on the North Yorkshire Moors.

Thursday's EU elections, and the performance of UKIP, will be relevant to Britain's future relations with America. The US has made clear it would prefer Britain to remain in the EU.

The SNP wants an independent Scotland to be a member of the EU.

Where does all this leave the UK's future role in the world, its relations with the US, and with the continent of Europe? These are questions the Westminster and Whitehall establishment prefers not to confront but ones that must be posed, considered, and answered.