The endeavour of Philip to substitute his will for self-government provoked a Catholic and aristocratic opposition, followed by a democratic and Protestant movement, which proved more difficult to deal with. The nobles were overcome by the strong measures of Alva. The Gueux were defeated by Don Juan and Farnese, after the recall of Alva. And it seemed, for many years, that the movement would fail. It is to the statesmanship of William the Silent, who was neither a great soldier nor a strong churchman, that they owed their success. He failed, indeed, to keep Protestants and Catholics together on a wide basis of toleration. In 1579 the southern provinces returned to Spain, and the northern provinces cast off their allegiance. But, by the union of Utrecht, they founded that confederacy which became one of the foremost powers in the world, and the first of revolutionary origin. The southern provinces remained Catholic. The northern were, in great measure, Protestant, but with a large Catholic population. William, the Stadtholder, was killed by an assassin in 1584, before his work was done. He had brought in Alencon, Elizabeth's suitor, that he might secure the help of France. But Alencon proved a traitor; and during the proconsulate of Farnese, Duke of Parma, the Spaniards gained much ground.
Philip II stood at the height of his power in the middle of the eighties. He had annexed Portugal, with its immense colonial empire. By the death of Alencon, the King of Navarre, who was a Huguenot, became the heir to the crown of France, and the Catholic party looked to Spain for their salvation. Now, after many patient years, he prepared for war with England. For Drake was ravaging Spanish territory; and an English army under Leicester, having occupied the Netherlands after the death of William, though they accomplished little, gave just cause for an open quarrel. Whenever, in the course of the Counter-Reformation, it came to a duel between Spain and England, the fate of Protestantism would be staked on the issue. That conflict was finally brought about, not by the revolt of the Netherlands, but by the most tragic of all histories, that begins at Holyrood with the murder of Riccio and ends twenty-one years later at Fotheringay.
When Mary Stuart came to Scotland the country had just become Protestant. She did not interfere with the settlement, but refused to permit the suppression of Catholicism, and became, in opposition to the most violent of the reformers, a champion of religious toleration. John Knox differed from all the Protestant founders in his desire that the Catholics should be exterminated, root and branch, either by the ministry of State, or by the self-help of all Christian men. Calvin, in his letter to Somerset, went very far in the same direction, but not so far as this. The nobles, or rather the heads of clans, in whom the power of society resided, having secured the Church lands, were not so zealous as their preachers, and the queen succeeded in detaching them. Mary was religious without ferocity, and did not share the passions of her time. She would have been willing to marry Leicester, and to make herself dependent on English policy, but Elizabeth refused to acknowledge her right of succession, and drove her to seek connection with the Catholic Powers. She wished at one time to marry Don Carlos, that, having been Queen of France, she might become Queen of Spain. This was impossible; and so she became the wife of Darnley, who united the blood of the Tudors and the Stuarts. She belonged, on her mother's side, to the house of Guise, whose princes were leaders of the militant Counter-Reformation. The duke, who had slaughtered the Huguenots at Vassy, was now dead. But his brother, the Cardinal, who afterwards claimed the merit of a more signal massacre, was still an important personage in Church and State. Mary, appearing on this background of sanguinary uncles, was believed to be an adherent of their policy, and to take part in all extremes of the Catholic reaction.
Riccio, the Piedmontese secretary, through whom she corresponded with foreign princes, was hated accordingly; and Darnley, who attributed to the Italian's influence his own exclusion from power, consented that he should be made away with. The accomplices who wrought the deed took care that Mary should know that they acted with his approval; and when she found herself the wife of an assassin and a coward, the breach ensued which was sometimes dissembled but never repaired. Three months later their son was born, but Darnley was not present at the christening. His enemies advised the Queen to obtain a divorce, but she objected that it would injure the prospects of her son. Maitland then hinted that there might be other ways of getting rid of him. Mary did not yield consent; but the idea once started was followed up, and the king was doomed to death by what was called the Bond of Craigmillar.
At the end of 1566 he fell seriously ill at his father's house at Glasgow. Mary came, spent three days with him, and an explanation took place, amounting apparently to a reconciliation. Darnley was taken to Edinburgh, and lodged about a mile from Holyrood, at Kirk-o'-Field, where he was repeatedly visited by the queen. On the night of 9th February she went away to attend a ball, and three hours after she had left him his house was blown up, and he was found in the garden, strangled. Nobody doubted at the time, or has ever doubted since, that the crime was committed by the Earl of Bothwell, a rough and resolute soldier, whose ambition taught him to seek fortune as a supporter of the throne. He filled Edinburgh with his troops, stood his trial, and was at once acquitted. Thereupon his friends, and some who were not his friends, acting under pressure, resolved that he should marry the queen. As a widow, she was helpless. Bothwell possessed the energy which Darnley wanted, and, as he was a Protestant, the queen would be less isolated. He had killed her husband; but then her husband was himself a murderer, who deserved his fate. Bothwell, encouraged by many of the Lords, had only executed justice on a contemptible criminal. There was a debt of gratitude owing to him for what he had done.
Public decorum forbade that the queen should ostensibly accept the offer of a man who made her a widow ten weeks before. Therefore Bothwell waylaid the queen at the Brig of Almond, some miles from Edinburgh, dispersed her attendants, and carried her off to Dunbar. There was a difficulty about the marriage, because he was married already. He now procured a divorce, and, ten days after the outrage at Almond Brig, they reappeared at Edinburgh. The queen publicly forgave Bothwell for what he had done, made him a duke, and, on 15th May, three months after the explosion at Kirk-o'-Field, married him according to the Presbyterian rite. The significant sequence of these events gave an irresistible advantage to her enemies. It was an obvious inference that she had been a party to the murder of the king, when she was so eager to marry the man that slew him. The only answer would be by discarding him. Nobody could think the son safe in the hands of his father's murderer.
Either the Lords must get the queen into their power, or they must dethrone her and govern Scotland during the long minority of her son. The forces met at Carberry Hill. There was no fight. Mary hoped, by a temporary parting from her third husband, to save her crown. She passed into captivity, was shut up at Loch Leven, and compelled to abdicate. The Protestant interest was at last supreme.
Mary escaped from her island prison, gathered an army, gave battle at Langside, and lost it, and then, losing courage before her cause was helpless, fled to England, in the belief that Elizabeth would save her.
From the death of Darnley, still more after her Protestant marriage, she had ceased to be the champion of her own Church. That was again her position when she came to England. There, she was heir to the throne, and the centre of all the hopes and efforts to preserve or to restore Catholicism.
The story of Mary Stuart cannot be told without an understanding in regard to the Casket Letters. They are still the object of an incessant controversy, and the problem, although it has made progress of late, and the interest increases with the increase of daylight, remains unsolved. The view to be taken of the events depends essentially on the question of authenticity. If the letters are what they seem to be, the letters of the queen to Bothwell, then she is implicated in the murder of her husband. If they are not authentic, then there is no evidence of her guilt. Everybody must satisfy himself on this point before he can understand the ruin of the Catholic cause in Scotland and in England, and the consequent arrest of the Counter-Reformation in Europe.