Today’s arrest of Alex Salmond marks a new chapter in the police’s investigations and a move on from the botched nature of the Scottish government’s inquiry.

With luck, the investigation will be swift, but the allegations against Salmond have brought to the fore tensions within the party that threaten to split it down the middle, with the two great personalities of the independence movement staring across from either side.

The former Scottish first minister was charged with two counts of attempted rape and nine counts of sexual assault on Thursday. Speaking to the media outside court, he said: “I refute absolutely these allegations of criminality, and I’ll defend myself to the utmost in court.”

The political cracks have been showing for a while now. No sooner had the Scottish government inquiry into allegations of sexual harassment against Alex Salmond been found to be unlawful than there were calls for his immediate reinstatement to the party – despite the fact he was still under police investigation.

Meanwhile, this week it was revealed that the SNP website had been changed to erase Alex Salmond’s role in bringing the party to prominence. All mentions of Salmond had been removed. Instead, the page bizarrely details how the 2014 independence campaign was “spearheaded by the SNP and its then depute leader Nicola Sturgeon”.

It hasn’t always been this way. Indeed, the strength of the SNP’s unity had long been the subject of envious glances. Motions at their party conference usually passed unanimously, the message discipline of both its MSPs and MPs was renowned, and the executive dominance of Nicola Sturgeon universally acknowledged. Much of the SNP’s 21st century success can be owed to its transformation from a raucous protest party to a well-slicked and on-message political machine.

But the reason that machine is now threatening to grind to a halt goes beyond what happened today. Rather, the serious allegations against Salmond – and the terrible mishandling of those allegations by Sturgeon’s government – are only the catalyst to divisions that have been brewing for some time – and calls to mind the Blair-Brown conflict in New Labour. Most fundamentally, these are over independence. Salmond believes the Yes campaign rightfully won in 2014, but Westminster “tricked” voters at the last minute and snatched victory from him. Sturgeon has never offered such denials.

On Sunday, meanwhile Salmond called for an end to the “uncivil war” within the party, but also simultaneously pushed Sturgeon towards calling an early independence referendum – a move which she has consistently resisted. In the same way that the shared goal of an independent Scotland held the party together before the referendum – overriding other differences amongst members and candidates – the means to achieve that same goal has now left the party divided.

In pictures: Alex Salmond's campaign for Scottish independence Show all 9 1 /9 In pictures: Alex Salmond's campaign for Scottish independence In pictures: Alex Salmond's campaign for Scottish independence The campaign for independence Alex Salmond stepped down as Scotland's First Minister and the leader of the SNP after the country voted no to independence Getty Images In pictures: Alex Salmond's campaign for Scottish independence The campaign for independence Alex Salmond said he accepted 'the democratic verdict of the people' PA In pictures: Alex Salmond's campaign for Scottish independence The campaign for independence First Minister of Scotland Alex Salmond chats to school children at Strichen Primary School in Strichen PA In pictures: Alex Salmond's campaign for Scottish independence The campaign for independence Scotland's First Minister Alex Salmond delivers his final independence speech to supporters in Perth EPA In pictures: Alex Salmond's campaign for Scottish independence The campaign for independence On the last day of campaigning before the polling booths open, the SNP leader wrote to voters in a final attempt to convince them to vote for independence Getty In pictures: Alex Salmond's campaign for Scottish independence The campaign for independence It was decided to give Alex Salmond an extra year in government AFP In pictures: Alex Salmond's campaign for Scottish independence The campaign for independence Alex Salmond and Alistair Darling taking part in a live television debate in Glasgow on 25 August Getty Images In pictures: Alex Salmond's campaign for Scottish independence The campaign for independence Alex Salmond during the live television debate with Alistair Darling at the Royal Conservatoire of Scotland on 5 August in Glasgow Getty In pictures: Alex Salmond's campaign for Scottish independence The campaign for independence Scottish First Minister Alex Salmond presents the White Paper for Scottish independence Getty Images

These aren’t just empty words from an ex-leader. If you need proof of Salmond’s continuing popularity, consider how easily he raised over £100,000 for his legal fund, his supporters donating an average of £25 to ensure that the target was reached in only three days. He has supporters high up in the party hierarchy too. Former justice secretary Kenny MacAskill and former presiding officer Tricia Marwick have attended court hearings with Salmond.

Popular MP Joanna Cherry, meanwhile, has liked a tweet saying: “Personally, I would love to see @AlexSalmond back at the helm of the SNP and finally deliver us our independence #Indy2”. She also liked another story headlined “Alex Salmond tells Nicola Sturgeon to ‘focus on achieving independence’”.

More central than Salmond’s comments from the sidelines, however, is the grassroots changes which Sturgeon is having to grapple with. The 2014 referendum may have left the Acts of Union unscathed, but the forces the SNP unleashed that year still leave their mark on Scotland’s public sphere. Their membership, once fairly modest, is now claimed to be second only to the UK-wide Labour Party at around 125,000 members.

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This post-2014 new wave of activists are bent on independence and reigniting the Yes campaign, and Sturgeon has struggled to temper their expectations with her desire to wait for a better moment. More widely, the radical discourse in the build up to 2014 has reawakened political interest and made the electorate at large less deferential to authority. In 2015, these same forces catapulted the SNP to an unprecedented electoral victory. They now threaten to unravel the party.