By Westminster Editor James Cusick

It was not the telephone conversation the prime minister had wanted, or expected, for a late anniversary present.

On Friday afternoon, with Downing Street still reeling from the humiliation of the Henley-on-Thames by-election and Labour's fifth place and lost-deposit showing behind a racist BNP candidate, Gordon Brown took a call from Wendy Alexander.

In an ideal political world, a struggling PM may have expected a "keep your head up" message from his Scottish parliamentary leader. Even a personal apology from Alexander over her continuing calls for a Scottish independence referendum which did little to help Brown's fading authority over the last few months would have helped Brown's mood.

But with the PM down - 21 points behind David Cameron in the latest opinion poll - Alexander kicked. She was resigning as Labour's leader in the Scottish parliament. No amount of persuasion by Brown would change her mind. She was going after barely nine months in the job.

Her departure, with no obvious candidate among a limited talent pool of Labour MSPs, plunges Labour in Scotland into a deepening crisis. And what affects Scotland, affects Brown.

Losing control of Holyrood to the SNP last year could be put down to an anti-Blair vote. But with Brown using all of his power nine months ago to get her installed, unopposed, as Scottish leader, her departure damages Brown's authority in a territory once regarded as his personal, unassailable fiefdom.

Others believe Brown's grip over Scottish affairs has been a convenient myth, with Alexander's departure exposing the hard reality of a limited and declining influence where the Scottish parliamentary leader can ignore the impact her actions will have on the prime minister's national standing.

"Gordon Brown couldn't stop her because although Wendy is a Brownite, she doesn't have the same instinctive loyalty, the reciprocated loyalty, others have," said one source who has been close to Brown and Blair. "That showed itself in the way she unilaterally called, and repeated the call, for a referendum against an agreed policy. She was beyond Brown's control."

His failing authority reflected in opinion poll ratings, his parliamentary party in Westminster far from content over the way they were marshalled in the recent 42 days anti-terrorist vote, and re-emerging back-bench discontent over the remedies offered to deal with poverty fall-out from the abolition of the 10p tax rate, Gordon Brown badly needs the DMZ, the demilitarised zone, that will come with the summer recess next month.

Alexander had been expected to use Holyrood's summer break in the same way: to regroup, rethink, and come up with a new survival strategy. But according to one senior government adviser, the explanation of why she chose to go, rather than fight, is basic. "She lost the stomach for it. She no longer wanted to wake up and wait for the Scottish Sunday papers, for the petty sniping, for the diligent SNP's snapping attack dogs."

That Gordon Brown couldn't persuade her to stay came as no surprise to those who had a ringside seat during Henry McLeish's forced exit as first minister. One said: "Tony and Gordon told Henry McLeish to stay. He didn't listen. If you looked closely, his eyes were dead."

Downing Street, having watched and endured Alexander claim her calls for a referendum had full backing from the prime minister when there was none, will have mixed feelings about her going. Brown had little option but to say what he said publicly yesterday afternoon, praising her "outstanding" contribution, saying she would be missed, and thanking her for work in rebuilding the Scottish Labour Party since the last election.

In private, Number 10 will have to deal with the fallout of Alexander putting herself first and the Labour Party second, the complete opposite of what her brother, Douglas Alexander, the international development secretary, said in defending his sister's actions.

For Brown, Alexander's timing couldn't have been worse.

A managed transition for Labour in Holyrood is out of the question. Those in Westminster will hope that Iain Gray, MSP for Edinburgh Pentlands, succeeds where Alexander failed by offering what one called "a sane critique of the SNP in power". Gray is regarded in London as safe, experienced and competent. But in the substantial in-tray of the PM's immediate problems, a new Scottish leader is now just one issue among many: though Scotland now has another uncomfortable major hurdle for Brown to scale.

Having recently lost Gwyneth Dunwoody's safe seat of Crewe and Nantwich to the Conservatives, and last week coming a lame fifth in Henley-on-Thames, a by-election is the last thing Brown needed to unwrap as a late first anniversary gift. The resignation of David Marshall and his 13,500 majority in a rock-solid Glasgow constituency would once have been regarded as something Labour dealt with as easily as putting up an umbrella. Now as storms surround Brown with rumours of a newly organised high-profile challenge to his leadership, and the call from Lord Levy, Blair's "cashpoint" fundraiser, for MPs to consider if Brown is a leader worth keeping, a pre-recess poll that will test Labour's standing against the Nationalists in a heartland constituency is an unwanted headache.

A source in Tory central office in London said Brown was "almost crawling into Westminster's summer break", and that even if the Conservative chair, Caroline Spelman, was forced to resign over the so-called "nannygate" issue, it would be "but a ripple of temporarily felt good fortune".

Talk of a reshuffle, of bringing back the Blairites from the backbench wilderness, was supposed to be the agenda of the coming month or so. The eagerly-awaited Darzi reforms for the NHS in England and Wales are due this week, offering an opportunity for Brown to do what he said he'd do a year ago when he called off the election-that-never-was, namely, offer his "vision". Now the vision is likely to be delivered blurred against a backdrop of Shettleston and a by-election that will test if the SNP will do to Labour what the Tories did in Crewe and the BNP did in Henley.

Labour won't lose its deposit in Glasgow as it did in Henley. And it's highly unlikely that they can lose a 13,500 majority. But having watched the Liberal Democrats win in East Fife two years ago and overturn a majority 11,500, only one thing is certain inside 10 Downing Street at the moment - the holidays can't come a moment too soon.