Thomson came to his arduous task brimming with ambition and belief in his ability to cope with it. He realized to the full the difficulty of the problem set him and the credit which would accrue if he solved it. 'After fifteen years,' a friend wrote, 'you have now the golden opportunity of settling the affairs of Canada upon a safe and firm footing, ensuring good government to the people, and securing ample power to the Crown.' He was fully aware of this himself. 'It is a great field too,' he notes in his private Journal, 'if I can bring about the union of the provinces and stay for a year to meet the united assembly and set them to work'; and he contrasts the opportunity for distinction offered by the Canadian imbroglio with the tame possibilities of a subordinate position in the Cabinet, which would be his fate if he remained in England.

The new governor-general reached Quebec in H.M.S. Pique on October 17, 1839, after a stormy passage of thirty-three days. His first task in Canada was the same as Durham's—to acquaint himself with the actual conditions—and he flung himself into it with equal energy. Like Durham, too, he was ably assisted by capable men on his staff, notably T. W. C. Murdoch, his civil secretary, and James Stuart, the chief justice of Lower Canada. From the very first he won golden opinions from all sorts of persons. The tone of his proclamations, the courtesy and tact of his public utterances, his personal charm made him speedily popular. The party of Reform was conciliated because he was known to be in sympathy with the principles of Lord Durham's Report, while the Conservatives were pleased with his avowed purpose of strengthening the bonds between the colony and the mother country. Lower Canada was still a province without a constitution; but it must have some machinery of government. A makeshift for regular government was provided by a Legislative Council of fourteen persons of importance appointed by Sir John Colborne. Their agreement to the principles of union was soon obtained. The province now seemed tranquil and the governor-general hurried on to Upper Canada. His account of his journey from Montreal to Kingston—the changes and stoppages, the varieties of conveyance—illustrates vividly the difficulties of travel in those days.

At Toronto Thomson found a totally different set of conditions. Here was a constitution functioning and a legislature in session; but what a legislature! Split into half a dozen little cliques and factions, it was trying to work with no cabinet, no opposition, no party system—an ideal state of things to which some critics of present conditions would like to return. The office-holders, that is, the members of the government, took opposite sides in debate. The Assembly was a house divided and sub-divided against itself. There was a wide-spread and persistent clamour for 'responsible government,' but no one knew precisely what was meant by it. Who was to be 'responsible'? for what? and to whom? How was it possible to make the local government 'responsible' to the people of the colony without reducing the governor to a figurehead? If his authority were reduced to a shadow, what became of the 'prerogative' and British connection? Was not 'responsible government' simply the prelude to the absolute separation of the colony from the mother country? Then there was the question of the Clergy Reserves agitating every colonial breast. One-seventh of the public domain had been set aside for the support of a favoured church: a plain case of monopoly and privilege, said some; a wise provision for the maintenance of religion, said others. And the shadow of bankruptcy was hanging over the unhappy colony. The situation was one of the utmost difficulty, calling for an almost superhuman combination of ability, tact, and firmness. Here, as in Lower Canada, the governor-general's first effort was to obtain the consent of the people's representatives to the great change in the status of the province which the union would involve. He carried his point by meeting men and discussing the project with them—a process of education. Although there was some opposition on various grounds, reasonable and unreasonable, the Assembly finally consented to the following terms: first, each province was to have an equal number of representatives; secondly, a sufficient civil list was to be granted; thirdly, the debt incurred by Upper Canada for public works of common interest should be charged upon the revenue of the new united province. These terms could not be called ideal, especially in regard to Lower Canada; but union was the only alternative to benevolent despotism or civil war. In bringing the legislature of Upper Canada to consent to these terms Thomson had the valuable aid of the cohort of Moderate Reformers led by Baldwin and Hincks.

No inconsiderable part of the governor-general's task was a campaign of education in the ABC of responsible government. Those elementary ideas of party government now regarded as axiomatic had to be taught painfully to our rude forefathers in legislation. That the government should have a definite head or leader in the Assembly, who should speak for the government, introduce and defend its measures; that the officials of the government other than those holding permanent posts should form one body—a ministry—which should automatically relinquish office and power when it could no longer command a majority in the legislature, were practically new and by no means welcome ideas to the old-time law-makers of Canada. The natural corollary that the opposition also should be organized under a definite leader, who, on defeating the government, should assume the responsibility of forming a cabinet, was equally novel. Such a check on reckless criticism was sadly needed. Of the process by which Thomson achieved his ends even his fullest biography gives little information. There must have been endless conferences of homespun, honest farmers like Willson, men of breeding like Robinson, brilliant lawyers like Sullivan, plain soldiers like MacNab, with the little, sickly, understanding governor of the brilliant eyes, the charming manner, and the persuasive tongue. Of all the varied explaining, discussing, initiating, little record remains. But the work was done and the results are manifest to the world. The persuasive little man succeeded in persuading the law-makers of Upper Canada that the way out of their difficulties lay not through division but through union. He persuaded them to a change of status which was a reversal to the old status prior to the Constitutional Act, and also a prelude to that larger union of the British colonies in North America which was destined to embrace half the continent.

Having succeeded almost beyond belief in the first part of his mission, Thomson turned his attention to the next vexed question. This was the question of the Clergy Reserves. On this subject much ink had been spilt and much hard feeling engendered; and it still provokes not a little ill-directed sarcasm. The whole matter is in danger of being misunderstood, and eighteenth-century lawmakers are blamed for not possessing ideas a hundred years ahead of their times.

By the terms of the Constitutional Act of 1791 one-seventh of the public lands thereafter to be granted were devoted to 'the Support and Maintenance of a Protestant Clergy.' The provision was due, it seems, to the king himself, pious, homely 'Farmer George'; and to men of his mind no provision could have seemed more natural or right. 'Establishment' had been the rule from time immemorial. The Church of England was 'established,' that is, provided by law with an income in England, in Wales, and in Ireland. The 'Kirk' was similarly 'established' in Scotland. In British America itself the Church of Rome was 'established' very firmly in Lower Canada. What could be more natural for a Protestant monarch than to make provision for a 'Protestant Clergy' in a British colony settled by British immigrants, and purchased with such outpouring of British blood and British treasure? And what more ready and easy way could be found of providing for that 'clergy' than by endowing it with waste lands which taxed no one and which would increase in value as the country became settled? In its essence this endowment was a recognition of the value of the Christian religion in preserving the state. But trouble arose almost at once in the interpretation of the terms 'Protestant' and 'clergy.' Was not the Church of Scotland 'Protestant' as well as the Church of England? Were not the various species of 'Dissenters' also the most vigorous of 'Protestants'? On the other side it was asked, Was not the term 'clergy' applied exclusively to the ministers of the Church of England? It could not apply to any religious teachers outside the pale; those outside the pale never dreamed of applying it to themselves. Naturally other denominations wished to share in this most generous endowment; and quite as naturally the Church of England desired to stand by the letter of the law and hold what it had of legal right. Some extremists opposed any and all establishments, holding that the church should be independent of the state. Let the endowment be used for the sorely pinched cause of education, and let the ministers of all denominations depend solely on the Christian liberality of their people. Perhaps the extremists were in closest touch with the genius of the new land and the new institutions growing up in it. To the plain man in the pioneer settlement there seemed something feudal, something unjust, in creating a privileged church at the expense of all other churches. Pioneer life brings men back to primal realities. To the settler in the log-hut the externals of religion are apt to fade until all churches seem to be much the same: to set one above all the others seems in his eyes so unjust as to admit of no argument in its favour. Besides, he had a very real grievance: the reserved unoccupied lands interfered with his well-being; they came between farm and farm, increased his taxation, and prevented the making of the needful roads. How was he to get to market? to fetch supplies? To-day few will be found to argue for a state church; but it was not so in the twenties and thirties of the last century. The battle raged loud and long; and pamphleteer rent pamphleteer in endless, wordy warfare.

By 1817 the grievance had become clamant; and when that inquisitive agitator, Robert Gourlay, asked the farmers of Upper Canada what hindered settlement, he received the answer—Clergy Reserves. Two years later the Assembly asked for a return of the lands leased and the revenue derived from them. Up to this time the annual revenue had not exceeded £700. In the same year, 1819, the 'Kirk' parish of Niagara applied for a grant of £100, and the law-officers of the Crown supported the claim. This decision stirred up the Anglicans. They formed themselves into a corporation in each province to oversee the administration of the Clergy Reserves. Ownership in the lands was to be obtained, if obtained at all, through the establishment and endowment of separate rectories, as provided for in the original act. Why the directing minds among the Anglicans did not adopt this ready and easy method of obtaining at least the bulk of the disputed land is something of a mystery. Apparently they adopted a policy of all or none. Only in 1836, just before the outbreak of the rebellions, when political feeling was at fever pitch, did Sir John Colborne, at the bidding of Bishop Strachan, sign patents for forty-four parishes to be erected in Upper Canada. The total amount of land devoted to this purpose was seventeen thousand acres. 'This,' declared Lord Durham, 'is regarded by all other teachers of religion in the country as having at once degraded them to a position of legal inferiority to the clergy of the Church of England; and it has been most warmly resented. In the opinion of many persons, this was the chief predisposing cause of the recent insurrection, and it is an abiding and unabated cause of discontent.'

Thomson's way of dealing with this cause of discontent did not dispose of it for ever, but it at least provided a lenitive. With the business man's respect for property and vested interests, he was opposed to the diversion of the grant from its original purpose to the support of education. He used his powers of persuasion upon 'the leading individuals among the principal religious communities.' After 'many interviews' he secured the support of the religious communities to a measure which he had prepared. By the terms of this bill the remainder of the reserved land was to be sold and the proceeds were to form a fund, the income from which should be distributed annually among the Church of England, the Church of Scotland, and other specified religious bodies, 'in proportion to their respective numbers.' This measure was not really acceptable to the Reformers, who wanted to see the land used in the cause of education; it was distasteful to the Kirk men; it was gall and wormwood to extreme Anglicans like Bishop Strachan. None the less, the personal influence of the diplomatic, strong-willed little man carried it through; and although the Act itself was disallowed, on excellent grounds, by the Imperial government, as exceeding the powers of the provincial legislature, yet the Imperial parliament passed an Act exactly to the same effect. Thomson had applied a plaster to the sore.