November and retired from politics in 1886. McIlwraith returned to stand for Parliament in 1888, this time as member for North Brisbane. His "National Australia Party" won a majority in the elections and he again became Premier and Treasurer. He came into conflict with the colony's Governor, Sir Anthony Musgrave over the exercise of the royal pardon. Musgrave died in October and McIlwraith petitioned the new Colonial Secretary Lord Knutsford, to allow the Queensland government to be consulted on the choice of governor. Knutsford refused and appointed Sir Harry Blake. The local legislature problematically declined to ratify the appointment, but henceforth it was understood that the colonies would be consulted in vice-regal appoinyments. In November of that year ill-health forced McIlwraith to resign in favour of Boyd Dunlop Morehead, whereupon he travelled to China and Japan. After his return McIlwraith's relationship with his colleagues deteriorated, and in August 1890 he formed an alliance (later known as the "Continuous Ministry") with his erstwhile foe to become Treasurer in the government of Sir Samuel Griffith. In March 1893 Griffith stepped down to join the Supreme Court of Queensland and McIlwraith became Premier again. His health was still poor and in October he resigned in favour of Hugh Nelson, contenting himself with the cabinet position of Chief Secretary and secretary for railways until 29 March 1895. The Dictionary of Australian of Biography says: McIlwraith was a big man with big ideas, but his indifferent health did not allow him to successfully carry the full burden of them. He was rugged and masterful, possibly on occasions not over-scrupulous, with a habit of getting his own way by sheer force of character rather than by intellectual ability. For nearly 25 years he was one of the greatest personalities in Queensland. After politics Since 1888 the London directors of McIlwraith's Queensland Investment and Land Mortgage Co. had complained about the practices of the local board, and in 1892 they charged McIlwraith, Palmer and two others with fraud. The remaining years of his life were surrounded in financial scandal and large financial losses by institutions that he was involved with. Although McIlwraith left for England on 15 January 1895, he was still a minister of the Queensland cabinet until 25 November 1897 when the Labor Party with government support succeeded in passing a resolution that he should retire. On 9 December he resigned from the Executive Council.