As editor Scott initially maintained the Manchester Guardian's well-established moderate Liberal line, "to the right of the party, to the right, indeed, of much of its own special reporting". However, when in 1886 the whigs led by Lord Hartington and a few radicals led by Joseph Chamberlain, split the party, formed the Liberal Unionist Party and gave their backing to the Conservatives, Scott's Manchester Guardian swung to the left and helped Gladstone lead the party towards support for Irish Home Rule and ultimately the "new liberalism".
In 1886, Scott fought his first general election as a Liberal candidate, an unsuccessful attempt in the Manchester North East constituency; he stood again for the same seat in 1891 and 1892. He was elected at the 1895 election as MP for Leigh, and thereafter spent long periods away in London during the parliamentary session. His combined position as a Liberal backbencher, the editor of an important Liberal newspaper, and the president of the Manchester Liberal Federation made him an influential figure in Liberal circles, albeit in the middle of a long period of opposition. He was re-elected at the 1900 election despite the unpopular stand against the Boer War that the Guardian had taken, but retired from Parliament at the time of the Liberal landslide victory in 1906, when he was occupied with the difficult process of becoming owner of the newspaper he edited.