Early in 1836 his health had become so seriously affected by his official labours that he began to recognize the necessity of resigning his office, and of accepting some post which would not so severely tax his energies. He continued to discharge his official duties, however, until the reconstruction of Lord Melbourne's Administration in 1839, when he signified his wish to be relieved. He was offered a choice between the office of Chancellor of the Exchequer and that of Governor-General of Canada. He chose the latter, and having received his appointment and been sworn in before the Privy Council, he set sail from Portsmouth for Quebec on the 13th of September, which was the fortieth anniversary of his birth. He reached his destination after a tedious, stormy voyage, and assumed the reins of government on the 19th of October. He was well received in this country. The mercantile community of Canada were especially disposed to favour the appointment of a man who had himself been bred to commercial pursuits, and who would be likely to feel a more than ordinary interest in promoting commercial interests.
Canada was at this time in a state of transition. Owing to the strenuous exertions of the Reform party in this country, seconded by Lord Durham's famous "Report," the concession of Responsible Government and the union of the provinces had been determined upon by the Home Ministry. It was Mr. Thomson's mission to see these two most desirable objects carried out. He had a most difficult part to play. As a pronounced Liberal, he naturally had the confidence of the Reform party, but there were a few prominent members of that party who did not approve of the Union project, and he felt that he could not count upon their cordial support. True, the opponents of the measure constituted a very small minority of the Reform party generally; but there was another party from whom the strongest opposition was to be expected--the Family Compact. This faction was not yet extinct, though its days were numbered. It still controlled the Legislative Council, which body had already recorded a vote hostile to the Union. The situation was one calling for the exercise of great tact, and the new Governor-General proved himself equal to the occasion. He made no changes in the composition either of the Special Council of the Lower Province--a body formed under Imperial sanction by Sir John Colborne--or in that of the Legislative Council of Upper Canada. After a short stay at Quebec he proceeded to Montreal, and convoked the Special Council on the 11th of November. He laid before this body the views of the Imperial Ministry relating to the union of the Provinces, and the concession of Responsible Government. By the time the Council had been in session two days the majority of the members were fully in accord with the Governor's views, and a series of resolutions were passed as a basis of Union. This disposed of the question, so far as the Lower Province was concerned, and after discharging the Council from further attendance, Mr. Thomson proceeded to Toronto to gain the assent of the Upper Canadian Legislature. With the Assembly no difficulty was anticipated, but to gain the assent of the Tory majority in the Legislative Council would evidently be no easy matter, for the success of the Governor's policy involved the triumph of Reform principles, and the inevitable downfall of the Family Compact. The Governor's tact, however, placed them in an anomalous position. For several years past the Tory party had been boasting of their success in putting down the Rebellion, and had raised a loud and senseless howl of loyalty. They were never weary of proclaiming their devotion to the Imperial will, irrespective of selfish considerations. This cry, which had been perpetually resounding throughout the Province during the last three years, supplied the Governor with the means of bending to his pleasure those who had raised it. He delivered a message to the Legislature in which he defined the Imperial policy, and appealed in the strongest terms to those professions of loyalty which the Tory majority in the Council were for ever proclaiming. He also published a circular despatch from Lord John Russell, the tone of which was an echo of that of his own message. The Tory majority were thus placed on the horns of a dilemma. They must either display their much-vaunted loyalty, by acceding to the Imperial will, or they must admit that their blatant professions had been mere party cries to deceive the electors. Their opposition, moreover, would render necessary the resignation of their offices. With the best grace they could, they announced their intention to support the Imperial policy.