By 1595 Stanley was desperate and suffered a reproof from the Spanish governor of the Netherlands for his violent language against Elizabeth. In December 1596 he helped deliver a renegade Scottish courtier John Wemyss of Logie to the Count of Fuentes. He continued in military service for the Spanish and was opposed to King James I on his accession in 1603, but he soon sued for a pardon and seemed desirous of returning to England. Sir Robert Cecil exonerated him from complicity in the Gunpowder Plot, but he never gained permission to visit England and spent the rest of his life in relative obscurity. He maintained a close association with the Jesuits, and when he had fallen out with them, with the English Carthusians.