Both Lee, who died in 1868, and himself persevered in spite of opposition, and Story had the satisfaction of seeing their views prevail. In 1884 a lectureship was founded in memory of Lee, and Story delivered the first lecture in St. Giles's Cathedral, Edinburgh, in April 1886, his subject being 'The Reformed Ritual in Scotland.'
Story, who meanwhile proved himself an ideal country parson, gradually became a leader in the church courts. From 1863 to 1876 he attended the general assembly of the church in accordance with ordinary regulations, but through special provisions he was a regular member from 1877 onwards. He became one of the ablest debaters in the house, advocating useful measures and sensible reforms. His name is conspicuously associated with discussions on Sabbath observance, on the abolition of patronage, on the Free Education Act, on the adaptability of the Confession of Faith to modern conditions, and, notably, on the movement for disestablishment before and after 1885. In May 1886 he was appointed junior clerk to the general assembly and in 1894 he was moderator, closing the meetings with a lucid and stirring address on 'The Church of Scotland, its Present and its Future' Next year he became senior clerk of the assembly, holding the position for the rest of his life. From 1885 to 1889 he edited a magazine — first called 'The Scottish Church' and then 'The Scots Magazine' — primarily designed for support of the principles he upheld. He had grave doubts as to the wisdom of the Free Education Act, but resolved to make the best of it when it had passed, and he was chairman of Rosneath school board from its first meeting in March 1873 till he left the parish. In 1886 he succeeded John Caird [q. v. Suppl. I] as chaplain-in-ordinary to Queen Victoria, and the appointment was renewed in 1901 by King Edward VII.
On 9 Nov. 1886 Story became professor of church history in Glasgow University. While zealously performing his special work he readily responded to the numerous calls which the city made upon him. In 1895 he was one of several Scottish ministers who discussed presbyterian reunion at a conference held at Grindelwald. In 1897 he was the Baird lecturer and took for his theme 'The Apostolic Ministry in the Scottish Church.' He was one of the representative divines who convened at Iona, on 9 June 1897 — the anniversary of the death of Columba, 597 — to offer 'thanksgiving for the introduction of the Gospel into our land.' Meanwhile he actively interested himself in the position of the church in the Highlands and in India, and in the Layman's League and home missions.
In 1898 Story was appointed principal of Glasgow University in succession to Dr. John Caird [q. v. Suppl. I]. In 1901 the ninth jubilee of the university was celebrated under his presidency. To his exertions was largely due the provision of new university buildings, mainly for medical and scientific purposes. At the same time he was a convinced champion of 'the humanities,' and his tenure of office was not free from friction with students. With the Carnegie Trust for the benefit of the Scottish Universities he was not in full sympathy, partly because of the exclusion of literary studies from its scope, but chiefly owing to its haphazard scheme for the payment of fees; but he fully recognised its value as a means of encouraging post-graduate research. After a period of gradually declining strength he died on 13 Jan. 1907, and was interred in the family burying-ground at Rosneath.
Story was made hon. D.D. of Edinburgh in 1874; hon. LL.D. of Michigan University, U.S.A. in 1887; hon. LL.D. of St. Andrews in 1900. He was also a fellow of the Scottish Society of Antiquaries, and he reached high degree as a freemason.
Story's chief publications were: 1. 'Memoir of [his father] the Rev. Robert Story,' Cambridge, 1862, an admirable contribution to ecclesiastical biography. 2. 'The Life and Remains of Robert Lee, D.D.,' 1870. 3. 'William Carstares: a Character and Career of the Revolutionary Epoch (1649-1715),' 1874, a survey of church and state in a time of transition. 4. 'The Apostolic Ministry of the Scottish Church' (Baird lecture), Glasgow, 1897. Other works were 'Christ the Consoler, or Scripture Hymns and Prayers for Times of Trouble and Sorrow' (Edinburgh, 1865); 'Creed and Conduct,' a collection of sermons (Glasgow, 1878; new edit. 1883); 'Saint Modan of Rosneath: a Fragment of Scottish Hagiology' (1878); and 'Health Haunts of the Riviera and South-West of France' (1881), the fruit of a continental holiday. Story edited a 'History of the Church of Scotland' (4 vols. 1890-91).
A portrait, presented by friends and painted in 1890 by Sir Philip Burne-Jones, and a study by John Bowie, A.R.S.A., for a group of Queen's chaplains, belong to the family. Two portraits in oil, by Sir George Reid, P.R.S.A., were prepared respectively for the Church of Scotland (now at 22 Queen
