[1] Thomas's confession implicated James VI of Scotland, who wrote several letters to Elizabeth to ensure his rights to English throne were unharmed.
[6] Crawforth was encouraged to implicate Thomas and assist in his capture by Edward Grey of Howick, constable of Morpeth Castle and depute Border Warden.
[16][17] An English diplomat in Edinburgh, George Nicolson, discovered that James VI had heard of Thomas's confession in April and believed Elizabeth I kept it secret in order to use it against him in the future.
[20] Nicolson worried that the ambassadors Peter Young and David Cunningham, Bishop of Aberdeen, sent by James VI to Denmark and to German princes in the wake of the visit of Anne of Denmark's brother the Duke of Holstein to request their future support for his succession to the throne of England would now spread news of "griefs and slanders" suffered by James because of the Valentine Thomas affair.
[21][22] It was reported in June 1598 that James VI had been told that William Cecil thought the issue was of low importance, that Thomas was "but a knave" and could be released.
[23] Edward Bruce told George Nicolson that James was still displeased by the affair, focussing on the failure of the English ambassador William Bowes to keep him informed.
[24] James prepared to send diplomats including David Foulis to London to try and resolve the situation, and ensure that the king's honour was not dented.
James VI was informed that Valentine Thomas had written a poem with charcoal on a chimney breast at the Tower of London:I shot at a fair white: And in loosing of my arrowMy elbow was wrested.
[32] A letter to Foulis from James Elphinstone mentions proposals to send Thomas as a prisoner to Scotland, where he could be interrogated with torture under English supervision and returned to England for execution.
[33] Foulis continued his work in London and sent reports back to Scotland by the usual land route, some countersigned by Sir Robert Cecil, and others were sent more securely by sea.
He wanted a signed statement, to the effect that Thomas was no more than a vagabond, guilty of various crimes, who had been to Scotland and hoped to avoid execution by making allegations about James VI.
[34] A statement of the key points of the confession dated 20 December 1598 was witnessed by John Peyton, Edward Coke, Thomas Fleming, Francis Bacon, and William Waad.
[35][36] Elizabeth wrote to Nicolson that she considered that James's propositions made by his ambassadors to Christian IV of Denmark and the German princes (concerning the English succession) were composed when he was "transported at that time with sudden and unjust rumours".
[42][43] Researchers at the British Library in 2023 discovered that amongst other revisions the chronicle writer William Camden had abbreviated his account of the Valentine Thomas affair for the publication of his Annals of the Reign of Elizabeth I.