The Scottish Parliament of May-July 1695, held while William was abroad, saw the beginning of evils for Scotland. The affair of Glencoe was examined into by a Commission, headed by Tweeddale, William's Commissioner: several Judges sat in it. Their report cleared William himself: Dalrymple, it was found, had “exceeded his instructions.” Hill was exonerated. Hamilton, who commanded the detachment that arrived too late, fled the country. William was asked to send home for trial Duncanson and other butchers who were with his army. The king was also invited to deal with Dalrymple as he thought fit. He thought fit to give Dalrymple an indemnity, and made him Viscount Stair, with a grant of money, but did not retain him in office. He did not send the subaltern butchers home for trial. Many years later, in 1745, the MacIans insisted on acting as guards of the house and family of the descendant of Campbell of Glenlyon, the guest and murderer of the chief of Glencoe.

Perhaps by way of a sop to the Scots, William allowed an Act for the Establishment of a Scottish East India Company to be passed on June 20, 1695. He afterwards protested that in this matter he had been “badly served,” probably meaning “misinformed.” The result was the Darien Expedition, a great financial disaster for Scotland, and a terrible grievance. Hitherto since the Union of the Crowns all Scottish efforts to found trading companies, as in England, had been wrecked on English jealousy: there had always been, and to this new East India Company there was, a rival, a pre-existing English company. Scottish Acts for protection of home industries were met by English retaliation in a war of tariffs. Scotland had prohibited the exportation of her raw materials, such as wool, but was cut off from English and other foreign markets for her cloths. The Scots were more successful in secret and unlegalised trading with their kinsmen in the American colonies.

The Scottish East India Company's aim was to sell Scottish goods in many places, India for example; and it was secretly meant to found a factory and central mart on the isthmus of Panama. For these ends capital was withdrawn from the new and unsuccessful manufacturing companies. The great scheme was the idea of William Paterson (born 1658), the far-travelled and financially-speculative son of a farmer in Dumfriesshire. He was the “projector,” or one of the projectors, of the Bank of England of 1694, investing £2000. He kept the Darien part of his scheme for an East India Company in the background, and it seems that William, when he granted a patent to that company, knew nothing of this design to settle in or near the Panama isthmus, which was quite clearly within the Spanish sphere of influence. When the philosopher John Locke heard of the scheme, he wished England to steal the idea and seize a port in Darien: it thus appears that he too was unaware that to do so was to inflict an insult and injury on Spain. There is reason to suppose that the grant of the patent to the East India Company was obtained by bribing some Scottish politician or politicians unnamed, though one name is not beyond probable conjecture.

In any case Paterson admitted English capitalists, who took up half of the shares, as the Act of Patent permitted them to do. By December William was writing that he “had been ill-served by some of my Ministers.” He had no notice of the details of the Act of Patent till he had returned to England, and found English capitalists and the English Parliament in a fury. The Act committed William to interposing his authority if the ships of the company were detained by foreign powers, and gave the adventurers leave to take “reparation” by force from their assailants (this they later did when they captured in the Firth of Forth an English vessel, the Worcester).

On the opening of the books of the new company in London (October 1695) there had been a panic, and a fall of twenty points in the shares of the English East India Company. The English Parliament had addressed William in opposition to the Scots Company. The English subscribers of half the paid up capital were terrorised, and sold out. Later, Hamburg investments were cancelled through William's influence. All lowland Scotland hurried to invest-in the dark-for the Darien part of the scheme was practically a secret: it was vaguely announced that there was to be a settlement somewhere, “in Africa or the Indies, or both.” Materials of trade, such as wigs, combs, Bibles, fish-hooks, and kid-gloves, were accumulated. Offices were built-later used as an asylum for pauper lunatics.

When, in July 1697, the secret of Panama came out, the English Council of Trade examined Dampier, the voyager, and (September) announced that the territory had never been Spain's, and that England ought to anticipate Scotland by seizing Golden Island and the port on the mainland.

In July 1698 the Council of the intended Scots colony was elected, bought three ships and two tenders, and despatched 1200 settlers with two preachers, but with most inadequate provisions, and flour as bad as that paid to Assynt for the person of Montrose. On October 30, in the Gulf of Darien they found natives who spoke Spanish; they learned that the nearest gold mines were in Spanish hands, and that the chiefs were carrying Spanish insignia of office. By February 1699 the Scots and Spaniards were exchanging shots. Presently a Scottish ship, cruising in search of supplies, was seized by the Spanish at Carthagena; the men lay in irons at Seville till 1700. Spain complained to William, and the Scots seized a merchant ship. The English Governor of Jamaica forbade his people, by virtue of a letter addressed by the English Government to all the colonies, to grant supplies to the starving Scots, most of whom sailed away from the colony in June, and suffered terrible things by sea and land. Paterson returned to Scotland. A new expedition which left Leith on May 12, 1699, found at Darien some Scots in two ships, and remained on the scene, distracted by quarrels, till February 1700, when Campbell of Fonab, sent with provisions in the Speedy Return from Scotland, arrived to find the Spaniards assailing the adventurers. He cleared the Spaniards out of their fort in fifteen minutes, but the Colonial Council learned that Spain was launching a small but adequate armada against them. After an honourable resistance the garrison capitulated, and marched out with colours flying (March 30). This occurred just when Scotland was celebrating the arrival of the news of Fonab's gallant feat of arms.

At home the country was full of discontent: William's agent at Hamburg had prevented foreigners from investing in the Scots company. English colonists had been forbidden to aid the Scottish adventurers. Two hundred thousand pounds, several ships, and many lives had been lost. “It is very like 1641,” wrote an onlooker, so fierce were the passions that raged against William. The news of the surrender of the colonists increased the indignation. The king refused (November 1700) to gratify the Estates by regarding the Darien colony as a legal enterprise. To do so was to incur war with Spain and the anger of his English subjects. Yet the colony had been legally founded in accordance with the terms of the Act of Patent. While the Scots dwelt on this fact, William replied that the colony being extinct, circumstances were altered. The Estates voted that Darien was a lawful colony, and (1701) in an address to the Crown demanded compensation for the nation's financial losses. William replied with expressions of sympathy and hopes that the two kingdoms would consider a scheme of Union. A Bill for Union brought in through the English Lords was rejected by the English Commons.

There was hardly an alternative between Union and War between the two nations. War there would have been had the exiled Prince of Wales been brought up as a Presbyterian. His father James VII. died a few months before William III. passed away on March 7, 1702. Louis XIV. acknowledged James, Prince of Wales, as James III. of England and Ireland and VIII, of Scotland; and Anne, the boy's aunt, ascended the throne. As a Stuart she was not unwelcome to the Jacobites, who hoped for various chances, as Anne was believed to be friendly to her nephew.

In 1701 was passed an Act for preventing wrongous imprisonment and against undue delay in trials. But Nevile Payne continued to be untried and illegally imprisoned. Offenders, generally, could “run their letters” and protest, if kept in durance untried for sixty days.

The Revolution of 1688-89, with William's very reluctant concessions, had placed Scotland in entirely new relations with England. Scotland could now no longer be “governed by the pen” from London; Parliament could no longer be bridled and led, at English will, by the Lords of the Articles. As the religious mainspring of Scottish political life, the domination of the preachers had been weakened by the new settlement of the Kirk; as the country was now set on commercial enterprises, which England everywhere thwarted, it was plain that the two kingdoms could not live together on the existing terms. Union there must be, or conquest, as under Cromwell; yet an English war of conquest was impossible, because it was impossible for Scotland to resist. Never would the country renew, as in the old days, the alliance of France, for a French alliance meant the acceptance by Scotland of a Catholic king.

England, on her side, if Union came, was accepting a partner with very poor material resources. As regards agriculture, for example, vast regions were untilled, or tilled only in the straths and fertile spots by the hardy clansmen, who could not raise oats enough for their own subsistence, and periodically endured famines. In “the ill years” of William, years of untoward weather, distress had been extreme. In the fertile Lowlands that old grievance, insecurity of tenure, and the raising of rents in proportion to improvements made by the tenants, had baffled agriculture. Enclosures were necessary for the protection of the crops, but even if tenants or landlords had the energy or capital to make enclosures, the neighbours destroyed them under cloud of night. The old labour-services were still extorted; the tenant's time and strength were not his own. Land was exhausted by absence of fallows and lack of manure. The country was undrained, lochs and morasses covered what is now fertile land, and hillsides now in pasture were under the plough. The once prosperous linen trade had suffered from the war of tariffs.

The life of the burghs, political and municipal and trading, was little advanced on the mediæval model. The independent Scot steadily resisted instruction from foreign and English craftsmen in most of the mechanical arts. Laws for the encouragement of trades were passed and bore little fruit. Companies were founded and were ruined by English tariffs and English competition. The most energetic of the population went abroad, here they prospered in commerce and in military service, while an enormous class of beggars lived on the hospitality of their neighbours at home. In such conditions of inequality it was plain that, if there was to be a Union, the adjustment of proportions of taxation and of representation in Parliament would require very delicate handling, while the differences of Church Government were certain to cause jealousies and opposition.