After years of scandal and intrigue, the Scottish National party has not lost its ability to shock. The UK Covid Inquiry has moved to Edinburgh for three weeks and in the process has exposed Nicola Sturgeon’s government to some robust scrutiny. The verbose, preening Hugo Keith has been replaced with Jamie Dawson, a more incisive KC. What he has uncovered has been a revelation.

That Sturgeon deleted her WhatsApp messages is bad enough. The ability to learn from the decision-making process is vital, so for a senior minister to wipe records like these can be seen as a conspiracy against the public. But as we have learned this week, the civil service in Scotland was also deeply complicit.

The inquiry has revealed the SNP’s priority is to advance the cause of independence at all costs

Humza Yousaf, the First Minister, was health secretary at the time. He was given advice from officials on how to dodge Covid mask laws. ‘Have a drink in your hands at all times,’ said Jason Leitch, the national clinical director. ‘Then you’re exempt.’ Leitch confides in another message that deleting messages has become his ‘pre-bed ritual’. Gregor Smith, Scotland’s chief medical officer, urged other civil servants to delete WhatsApp exchanges ‘at the end of every day’.

One of Scotland’s most senior civil servants, Ken Thomson, should have been stamping out this attitude. Instead, he warned colleagues that their chat ‘is discoverable under FOI’ and wanted them to ‘know where the “clear chat” button is’. In what may be one of the most memorable phrases uncovered by the inquiry on either side of the border, Thomson boasted to colleagues that ‘plausible deniability are my middle names’.

This was quite a moment, not just for the Covid Inquiry but for devolution in general. Thomson was once the right-hand man of the straight-playing Donald Dewar, regarded as a founding father of devolution. To see him talking like an SNP hit man, adopting a modus operandi that has more in common with gangsterism than government, is indicative of the deeper decay with which Scots are all too familiar. Rather than providing good government, the SNP has specialised in covering up bad government and, as the inquiry has revealed, its priority is to advance the cause of independence at all costs.

When I was a reporter in the early days of the Scottish parliament, a nationalist MSP explained the thinking to me. They had once seen devolution as a trap to enmesh them in UK government, but then realised that it could be used as a device to advance the idea of nationhood. In a devolved Scotland, any crisis could be turned to their advantage. If, say, there was an earthquake in Armenia, Scottish aid could take off from Edinburgh airport flying the Scottish flag. Small steps but, for the SNP, this was the mission.

When Covid struck, in public Sturgeon disparaged the idea of a ‘race’ with England to control the virus. In private, officials were told to make comparisons that showed Scotland in a better light. Sturgeon was adept at making herself the face of the crisis response, and her daily televised press conferences continued long after Boris Johnson’s had stopped. Her aim was to project herself as the calmer, more assured leader. At one stage, Sturgeon claimed that the prevalence of Covid was ‘five times lower’ in Scotland than in England, where there was a ‘shambolic decision-making process’.

There was no evidence for the claim, but it worked. Polls showed support for independence growing, in a way it had failed to do after Brexit. Naturally, Sturgeon said this was the last thing on her mind: anyone making ‘constitutional or political’ arguments was ‘in the wrong place completely and has found themselves completely lost’, she said. ‘We’re not dealing with politics at the moment,’ she assured the nation.

We now know that she was speaking fresh from a cabinet meeting where her ministers had formally agreed that ‘consideration be given to restarting work on independence and a referendum’. Arguments for separation were to be based on the ‘experience of the coronavirus crisis’. This was not just an afterthought. Politicisation of the crisis had become a cabinet strategy.

Sturgeon had toyed with breaking completely with the UK strategy. ‘Our objective has to be to eliminate,’ she declared, though Scotland’s chief medical officer told the inquiry that he ‘regularly’ told Sturgeon that this was a non-starter. She had enlisted Devi Sridhar, an Edinburgh academic who was an advocate of the ‘zero Covid’ strategy. Sturgeon asked Sridhar to give advice via her SNP email, which is not monitored by officials. (‘Don’t worry about protocol,’ she told Sridhar. ‘You can send it to me privately.’)

In retrospect, Sturgeon’s approach was clearly nonsensical: Australia and New Zealand had pursued ‘zero Covid’ strategies, but because of their geography, draconian lockdowns were possible. For Scotland and England to follow down this road was always implausible. But this was the SNP’s aim: to differentiate between the two.

Had attention instead been given to protecting care-home residents (whose death rate was higher in Scotland) many more lives could have been saved. Scotland might genuinely have had a better outcome than England. But this is just one of the many missed opportunities.

The year marks the 25th anniversary of devolution, brought in by Tony Blair in the belief that Scotland would be better served by ‘home rule’ than by the supposedly remote legislators of Westminster. The newly designed Holyrood system was supposed to be an improvement upon the antiquated House of Commons and the Lords. A unicameral chamber would make better, more streamlined decisions, it was thought. There would be more scrutiny, more openness and more accountability.

In seeking to solve the old ‘democratic deficit’, devolution has created a new one

How naive that all seems. The Scottish parliament had a few stars but it dredged too many candidates from council chambers, and there was from the outset an unhealthy clannishness. At first it was a Scottish Labour establishment, which used its powers to reject Blairite reform on health and education. This was ironic. In England, power was being devolved to parents through the school choice agenda. In Scotland it was being hoarded by a new centralised state.

The SNP only made centralisation worse. The eight regional police forces were merged into a new, nationwide (and, it soon turned out, dysfunctional) Police Scotland. A revolution was imposed on schools with the new ‘curriculum for excellence’, which teachers soon began to say was having calamitous consequences. Drugs deaths, already the worst in the UK, trebled. The highest state spending in the UK was not translating into better services.

This new establishment has been marked by the erasure of the distinction between the governing party and the apparatus of government. When Ken Thomson was made ‘director-general for strategy and external affairs’, for example, he proclaimed that the inclusion of ‘strategy’ in his title was ‘a shorthand for constitutional change’. The term ‘gets me through some doors in Whitehall’, he said. ‘Then they discover that I’m actually there to talk about breaking up the kingdom.’ When a video of his remarks leaked, it was the clearest sign that the Scottish government machine had become a facilitator of nationalism rather than of good government.

Another particularly stark example of this is the near-total absence of ‘ministerial directions’ since the SNP came to power. These are written orders issued when ministers wish to override a permanent secretary’s objections to a proposed item of spending.

The Institute for Government once ran a study and found 52 ministerial directions to Whitehall departments since 2010, suggesting that UK civil servants are more than prepared to challenge ministers’ policy choices. In Holyrood there had been only one: in August 2007, three months after the SNP came to power. This was despite the SNP-run Scottish government authorising a raft of controversial projects in the past 17 years, including the production of pro-independence policy papers. (This is a political issue which the civil service should stay out of.)

The Alex Salmond scandal showed the extent to which parliament and its committees (which have fewer powers than Westminster) lack the tools to hold ministers to account. He said he was being framed on sexual assault charges so he could be imprisoned and removed as a political threat to Sturgeon. But his evidence was redacted and a Holyrood committee was warned they could not refer to it without fear of prosecution. MSPs do not have the protection of parliamentary privilege, which allows Westminster MPs to say what they like.

The policies Holyrood has been coming out with – gender recognition, a named government guardian for every child, a referendum bill without Westminster consent – have been so inept and error-strewn that they are thrown out by the courts. These weaknesses should be spotted and corrected by parliament – but devolution has left Scotland with a powerful executive, a weak legislature and no checks and balances.

Reporting restrictions limit what can be said about the current investigation into what police describe as the possible ‘misuse of funds and potential embezzlement’ that saw the arrests of both Sturgeon and Peter Murrell, her husband, who was also the SNP’s chief executive. The £110,000 white camper van at the centre of the fraud probe is still impounded in a police car park. The suggestion is of malpractice on a scale that compares with the worst any democracy has thrown up. As the Scottish Lib Dem leader Alex Cole-Hamilton remarked: ‘Even Richard Nixon didn’t destroy the Watergate tapes.’

Yousaf can hardly pose as a fresh face, given that he was health secretary during Covid and was then elected as the party leader with Sturgeon’s blessing. Those who are concerned that Scotland was run by a political machine can see, in Yousaf, the perfect machine candidate – and one who has filled his cabinet with similar loyalists. Kate Forbes came strikingly close to banishing him, winning 48 per cent of the vote. But SNP members voted for continuity Sturgeonism, with predictable results.

In seeking to solve the old ‘democratic deficit’, devolution has created a new one. The clique that now runs Scotland is un-able to distinguish between the objectives of a political party and the proper conduct of government. In the next election, perhaps both Labour and the Tories will promise Scots a form of constitutional repair – some steps to restore civil service neutrality, giving Holyrood more powers to hold the Scottish government to account.