The tragedy caused intense excitement throughout Scotland, and the investigation of the circumstances was followed with much interest in England also, where all the details were reported to Elizabeth's ministers. The preachers of the Kirk, whose influence in Scotland was too extensive for the king to neglect, were only with the greatest difficulty persuaded to accept James's account of the occurrence, although he voluntarily submitted himself to cross-examination by one of their number. Their belief, and that of their partisans, influenced no doubt by political hostility to James, was that the king had invented the story of a conspiracy by Gowrie to cover his own design to extirpate the Ruthven family. James gave some colour to this belief, which has not been entirely abandoned, by the relentless severity with which he pursued the two younger, and unquestionably innocent, brothers of the earl. Great efforts were made by the government to prove the complicity of others in the plot. One noted and dissolute conspirator, Sir Robert Logan of Restalrig, was posthumously convicted of having been privy to the Gowrie conspiracy on the evidence of certain letters produced by a notary, George Sprot, who swore they had been written by Logan to Gowrie and others. These letters, which are still in existence, were in fact forged by Sprot in imitation of Logan's handwriting; but the researches of Andrew Lang have shown cause for suspecting that the most important of them was either copied by Sprot from a genuine original by Logan, or that it embodied the substance of such a letter. If this be correct, it would appear that the conveyance of the king to Fast Castle, Logan's impregnable fortress on the coast of Berwickshire, was part of the plot; and it supplies, at all events, an additional piece of evidence to prove the genuineness of the Gowrie conspiracy.
Gowrie's two younger brothers, William and Patrick Ruthven, fled to England; and after the accession of James to the English throne William escaped abroad, but Patrick was taken and imprisoned for nineteen years in the Tower of London. Released in 1622, Patrick Ruthven resided first at Cambridge and afterwards in Somersetshire, being granted a small pension by the crown. He married Elizabeth Woodford, widow of the 1st Lord Gerrard, by whom he had two sons and a daughter, Mary; the latter entered the service of Queen Henrietta Maria, and married the famous painter van Dyck, who painted several portraits of her. Patrick died in poverty in a cell in the King's Bench in 1652, being buried as "Lord Ruthven." His son, Patrick, presented a petition to Oliver Cromwell in 1656, in which, after reciting that the parliament of Scotland in 1641 had restored his father to the barony of Ruthven, he prayed that his "extreme poverty" might be relieved by the bounty of the Protector.