It was Nick Robinson, the BBC's political editor, who set the hare in motion.

With an announcement from BAE Systems imminent, he reported from one of those highly placed sources to the effect that the Government was "deeply conscious" of something called "the politics of the Clyde".

Robinson and a host of others took this to be a reference to next year's September's independence referendum. On a first reading it seemed London was keen indeed not to upset Glasgow, the city in which the argument could yet be decided. Crippling or closing Govan and Scotstoun counted, it seemed, as poor politics.

But if that was so, where did smart thinking come in? Even if Whitehall deemed the risk of a Yes vote remote, it counted as cavalier to take chances with future naval planning for a remaining UK. BAE Systems might have talked, before and after, of "purely commercial" decisions, but the unwritten rule said that Britain did not build its warships in foreign countries.

In the ensuing game of bluff and double bluff, one fact could not be dodged. If shipbuilding came to an end at Portsmouth, only the Clyde would remain in these islands as a provider of sophisticated warships. Even if the English yard was mothballed, a large investment in time and money would be needed to turn it into a viable alternative to Govan. The referendum, that political choice, remained relevant.

But there were further risks. After the announcement, Portsmouth and its workers drew the instant, unforgiving conclusion that Scotland's gain - if you overlooked 800 Scottish jobs - was England's loss. At that moment it would have been a brave politician who advertised the benefits of "better together" on the Hampshire coast.

The political tide moved quickly. Primed, no doubt, by the utterances of Robinson's source, Tory MPs and London commentators decided within hours that the Scots were being bribed at the cost of an English naval tradition. It seemed too high a price to pay, as one columnist observed with no irony, "for keeping a few querulous Scots on side".

How, though, did Scotland feel about being "bribed", if that's what was going on? How grateful were Scots supposed to be for the loss of 800 jobs in a small country, given the assurance that the Clyde was the winner in any straight shipbuilding contest? To be granted as a favour something that is yours by right is never appealing. To have 800 lost jobs described as a victory is a strange sort of compensation.

So here came the real politics. How would the parties fighting the referendum argument manage perceptions? The Unionist side in particular had a complicated tale to tell. The narrative seemed to be ill-understood, even by the proponents of better together. Above all, they had to avoid a brute statement while somehow conveying its sentiment. They couldn't say "Vote No or Govan Gets It". But that was the general idea.

First, Ian Davidson, Labour MP for Glasgow South West, covered himself in something that wasn't glory by suggesting that a "break clause" should be inserted into future contracts for Type 26 frigates. The meaning was simple: if Scotland voted Yes in the referendum, Govan would lose the work. In essence, Davidson's own constituents would lose the work.

Alistair Carmichael, the Scottish Secretary, then demonstrated just how naked politics can become by stating that "if Scotland is no longer part of the country" - you knew what he meant - it would be "difficult to see how the [frigate] work would go to Scotland". The business case made by BAE Systems was simplified: "These contracts are on the Clyde because the Clyde is part of the UK."

Carmichael chose to ignore any problems associated with the end of shipbuilding at Portsmouth and did not dwell on Govan's merits. The referendum was central to his assessment. "If Scotland were to vote Yes," he observed, "then the rest of the UK would be looking for shipyards within their jurisdiction and, yes, you would think Portsmouth would be well placed in that circumstance."

Factually, this was on the wrong side of arguable. Politically, though Carmichael denied any such intention, it sounded like a threat. But it was a step beyond the usual claim that independence would not be in Scotland's interests. It amounted to a guarantee to that effect. The bribe had acquired an undertone liable to render the notion of better together as something like "Union-with-menaces".

Unionists would not accept that interpretation, of course, but nor do they explain why Labour have yet to object to the treatment of Portsmouth and the loss of 940 jobs in that city. Officially, the case is still being "examined". But unless we hear otherwise, we can presume that Better Together's lead party agrees with the Government and BAE Systems that the Clyde is the right choice.

Undaunted, Johann Lamont tried again at First Minister's Questions on Thursday. As she described matters, a Yes vote in the referendum would deprive Scotland of all influence over a UK government. Despite the certainty of 800 redundancies on the Clyde under the Union, Lamont declared that the independence movement's "prospectus for Scotland threatens their jobs".

Subsequently, Carmichael denied attempted blackmail. With hundreds of jobs to go, he discerned "a very positive situation", an "illustration of the opportunities that exist for Scotland and Scotland's industries as part of the United Kingdom". He could as well have said that shipbuilding will have it tough on both sides of the Border if it continues to depend on defence work alone.

The SNP have talked about the need for diversification on the Clyde as though the idea is new. Scotland's Government has suggested that an independent country might want five of the planned frigates. But the text and sub-text offered by the Better Together parties spare little room for what the SNP would like. A gamut is run. Union is good for Scotland, independence would be bad, and if voters refuse to grasp that lesson they will have to learn it the hard way.

Unionists would call that realism rather than a threat. Nevertheless, it marks a new phase in the independence argument. Some of us have been awaiting this for a while, this moment when matters become explicit, when a Davidson or a Carmichael makes it plain that London might choose to make life very difficult for an independent Scotland.

That's not a prediction. If you want one of those, it would state that independence will see an outbreak of common sense, that self-interest will prevail, not least in matters of military procurement and defence. But this has all been the merest rehearsal for the biggest row of all, the one that can't be avoided, the one called Faslane.

If the London Government meant to skewer the SNP by demonstrating why the Union works for Scotland, things have not gone to plan. Instead, underlying tensions within the relationship have been brought into the light. If Unionists meant to demonstrate that no one should play politics with jobs, meanwhile, they have chosen a strange way to illustrate the thesis.

Above all, we have seen how rough things are liable to get before Scotland makes its choice. Squeamishness is not advised.