Instead of housing the 13th century document in the court building, it will now be displayed in a specially-made vault in the castle prison, with its own entrance.
The vault would be placed in the unused male prison end of the building, which will need investment for alterations before opening to the public.
Mary Powell, Tourism Development Manager, said that although Plan B would not upset the Crown Court, the council still hopes to move the service out of the castle.
She said: “We are determined not to lose the opportunity to restore Lincoln Castle.
“Our top priority very much remains the relocation of the Crown Court, which we have certainly not given up on.
“However, with the Heritage Lottery Fund bid ready for submission, it is prudent to have a secondary option and we are consequently now working hard on a possible Plan B.
“This would involve opening up the old male prison to the public.
“It is a vast, well-lit space with a great atmosphere and potential, and is a fascinating building with its cast iron trusses and lattes.
“Investigations and discussions into this are at an early stage, as we need to assess factors such as the roof, which may need around £1 million spending on it.
“Incorporating Magna Carta into this setting would be a fitting location to display such a proud piece of history.
“We’re also looking into how public tours could work in the area and this plan would offer an excellent visitor experience.
“Use of the prison was not originally in our plans due to the costs but, if the Crown Prosecution Service do not choose to remove the court, the prison becomes an option.
“Essentially though, Plan B just means we restore the elements of the castle in a different order; we are still determined that it will be worked on in tandem with Plan A – the ultimate removal of the court.”
Lincoln currently houses one out of four of the original surviving versions of the Magna Carta. The others are in Salisbury Cathedral, Westminster and the British Library.
Other surviving versions can be found at Durham Cathedral, Hereford Cathedral, Oxford’s Bodleion Library, Camberra, Australia and Washington DC in the US.
Lincoln's copy of the Magna Carta currently on display.
In the meantime, work will begin on the revamp of the South Curtain in the Castle and adding a walkway, so visitors can walk all the way around the top of the wall.
Powell said: “The contractor will be appointed in March and they plan to begin in May after the last frosts.
“All the potential contractors are experienced with working on historic buildings. For the external repairs we are very grateful to the Drury Lane residents for their understanding.”
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