MSPs have rejected a Tory motion calling for indyref2 to be scrapped.
Instead, an SNP amendment stating "there can be no justification whatsoever to deny people in Scotland their democratic rights" if there is a pro-independence majority after May's Holyrood election passed by 65 votes to 56.
Over the weekend, the SNP revealed a new roadmap setting out how they would secure a vote on Scottish independence - even if Downing Street refuse to consent.
Last year the Scottish Government was working on legislation to allow a second independence referendum, though it was suspended in March as “a result of the need to deploy as many civil servants as possible to work on Scotland’s response to the pandemic”.
But in last September’s Programme for Government, Nicola Sturgeon said independence was vital to reversing Brexit and allowing Scotland to rejoin its European allies.
She told MSPs: “That is why, before the end of this Parliament, we will publish a draft bill, setting out the proposed terms and timing of an independence referendum, as well as the proposed question that people will be asked in that referendum. And then at next year’s election, we will make the case for Scotland to become an independent country, and seek a clear endorsement of Scotland’s right to choose our own future.”
The roadmap said this bill would be enacted “if an SNP Scottish Government is re-elected with a majority to do so (either as a result of gaining an overall majority or if it had such a majority as a result of support from another pro-independence party)”.
However, it says the referendum should be held after the pandemic, at a time to be decided by the democratically elected Scottish Parliament.
The initial Tory motion had suggested the Scottish Government needed to choose between creating a vaccine taskforce and an independence referendum.
It said "planning an independence referendum in 2021, during an ongoing global pandemic, would be reckless and damaging".
Opening the debate, the Scottish Tory health spokesman Donald Cameron said: "After everything Scotland has gone through and is still going through, it simply beggars belief that this Government thinks it's right to talk about IndyRef2 at this point in time.
"For some completely unfathomable reason, the SNP have chosen the middle of a global pandemic as the right time to serialise their never-ending obsession with independence.
"That's not just unfathomable, but unforgivable."
Cameron suggested it was "abundantly clear" Scots wanted the Government to "focus on rolling out vaccines, reducing the numbers of deaths and cases of Covid-19 and rebuilding our economy".
He added: "Whatever your view on the constitutional debate, we urge the Scottish Government: pause, reflect and realise what is at stake if we take our eye off the ball at this critical juncture of the pandemic.
"Now is not the time to divide communities all over again.
"Instead, now is the time to unite people across this country, as we hopefully enter the final chapter of our collective struggle against the pandemic that has brought so much sadness across Scotland."
The SNP Constitution Secretary Michael Russell rejected Cameron's criticism of the Scottish Government's handling of the Covid crisis.
He said: "The Government is doing precisely what the motion calls for; we are tackling pandemic investing economic recovery, delivering a vaccination programme which is saving lives and helping Scotland's return to some form of normality over the coming months."
Russell added:"Sadly the pandemic is not the only issue the country is having to deal with.
"The pandemic is an external crisis, but there's another crisis has been inflicted on us by the Tory UK government.
"The UK Tory insistence, backed by the Scottish Tories, on a reckless decision to press on with the end of the transition period for leaving the EU - even in the face of this unprecedented economic, social and health crisis - has caused, is causing, and will cause untold economic and social damage."
Russell continued: "It is for the people of Scotland to decide what country and economy should be built following the pandemic.
"That is why, if there is in the next parliament a majority for an independence referendum that would allow us to become a normal small state within Europe, living in harmony and equity with our neighbours, then I believe that Parliament has an absolute right to take the matter forward. That's democracy."
Labour leadership hopfeful Monica Lennon said Covid didn't "care about politics or the constitution."
"It's a virus that has and kills regardless of your opinion," she added.
"Getting Scotland vaccinated should be uniting this Parliament that's why it is so disappointing that the Scottish conservatives are using precious parliamentary team to raise constitutional issues," Lennon told MSPs. "Parliament should be focused on scrutinising the SNP government's covid response and improving it.
"We badly need a plan to eliminate COVID and safely ease restrictions. People in our country want to be brought together. The priority for all of us needs to be getting the vaccine into people's arms. That's what the people of Scotland want to see action on."
Lib Dem leader Willie Rennie was also critical of the SNP's roadmap. He said: "It will take all our combined efforts and ingenuity, our commitment to recover from this pandemic.
"It will take our undivided attention, our needle sharp focus. So it beggars belief that anyone, even the most committed and dedicated supporer, that anyone should even suggest that as we start to plot a recovery, that this country should turn our attention to another independence campaign and referendum."
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