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Malcolm sailed for Bombay, but he was not clear of the Hooghly before he was hastily recalled on the arrival of news that Sir Harford Jones had reached Bombay and persisted in the design of proceeding to Persia, notwithstanding Malcolm's rebuff. Malcolm's expedition was first postponed and then abandoned, and in May 1809 he embarked for Madras.

At this juncture the Madras mutiny occurred, and shortly after his arrival Malcolm was despatched by Sir George Barlow to Masulipatam to deal with the revolt, which had broken out in that important military station against the authority of Colonel Innes, who was in command of the Madras European regiment there. Reaching Masulipatam, he found the garrison in a state of open and bold mutiny, and on the point of marching to join the subsidiary force at Hyderabad. It was loth even to admit him within the lines. He promptly delivered Colonel Innes from the garrison, convened a meeting of the officers, reasoned with them, and, while declining himself to give any pledge or assurance, prevailed on them to abandon for the present their intention of marching to Hyderabad. His principal object was to gain time, and in this he succeeded; but his proceedings were not approved by Sir George Barlow. He was superseded by General Pater, and on his return to Madras was coldly received. Barlow pursued the opposite policy of sternness and severity, and it met with success. Malcolm took the earliest opportunity of returning to diplomatic employment, and was again despatched to Persia in the end of the year (see justificatory pamphlet, Observations on the Disturbances in the Madras Army in 1809, 1812).

Sailing from Bombay on 10 Jan. 1810, it was not until 13 Feb. that he reached Bushire, but the interval was diligently employed in making progress with the ‘Political History of India,’ which he had begun in the previous year, and afterwards published in 1811. It was completed on 6 March, though he did not take his departure for Teheran till 15 April. The intricacies of Persian etiquette had occasioned this delay, but when he proceeded on his journey he was received not only with pomp, but with cordiality. At Teheran he was embarrassed by the presence of Sir Harford Jones, the king's ambassador to Persia, who exercised in that capacity superior authority over the mere envoy of the governor-general, and was exasperated by want of success in his mission and want of support from the East India Company. It was only after considerable negotiation that they were able to meet as friends and co-operate in politics. After Malcolm had been received with welcome and warmth by the shah, the news arrived that the British government, wishing to keep diplomatic relations with Persia in its own hands, and to withhold them from those of the governor-general, had appointed Sir Gore Ouseley ambassador to the court of the shah. His official position being thus extinguished, Malcolm decided to quit Persia at once, in spite of the shah's desire to retain him as a military adviser during the impending war with Russia. The order of the Lion and Sun of Persia having been created for his especial decoration, he was allowed to depart with that and other high honours at the end of July. He returned by way of Baghdad, where his presence and escort protected the British residency during a civil war between an incoming and an outgoing pacha, and he reached Bombay at the end of November. The sole result of this long and costly mission was the creation of a Persian order for the envoy by the shah, and the introduction of potatoes into Persia by the envoy (see, Mission to the Court of Persia; , Travels through Persia, 1812; Lord Minto in India, 1880).

Malcolm remained for some time at Bombay, passing his accounts through the official audit and composing his ‘History of Persia.’ Of the first the government officially recorded its censure that his expenditure was extravagant; for the second it granted him special allowance and a staff of transcribers, together with prolonged leave of absence from his post at Mysore. While occupied upon his history he also composed a justification of his conduct at Masulipatam during the mutiny in the Madras army. It was entrusted to Sir James Mackintosh for publication in England, and, by Malcolm's express desire, this took place before he himself arrived in England on furlough in July 1812. Malcolm now remained at home for nearly five years. During this time he formed various literary connections (, Memoir of John Murray, i. 236, 268), became acquainted with Sir Walter Scott, produced his ‘History of Persia’ in July 1815, with great success, and received the honorary degree of doctor of laws at Oxford in 1816. Shortly after his arrival he was knighted, received permission to wear the insignia of the order of the Lion and Sun in England, and in April 1815 was made a K.C.B. His views on the treatment of the Indian army were considered by the board of control, and he was examined before the House of Commons on various Indian topics in April 1813. Owing to his various missions and his careless habits he found himself in embarrassed circumstances. The Indian