At last the general discontent took shape in open resistance. The success of the French Huguenots in wresting the free exercise of their faith from the monarchy told on the Calvinists of the Low Countries. The nobles gathered in leagues. Riots broke out in the towns. The churches were sacked, and heretic preachers preached in the open fields to multitudes who carried weapons to protect them. If Philip's system was to continue it must be by force of arms, and the King seized the disturbances as a pretext for dealing a blow he had long meditated at the growing heresy of this portion of his dominions. Pius the Fifth pressed him to deal with heresy by the sword, and in 1567 an army of ten thousand men gathered in Italy under the Duke of Alva for a march on the Low Countries. Had Alva reached the Netherlands while Mary was still in the flush of her success, it is hard to see how England could have been saved. But again Fortune proved Elizabeth's friend. The passion of Mary shattered the hopes of Catholicism, and at the moment when Alva led his troops over the Alps Mary passed a prisoner within the walls of Lochleven. Alone however the Duke was a mighty danger: nor could any event have been more embarrassing to Elizabeth than his arrival in the Netherlands in the autumn of 1567. The terror he inspired hushed all thought of resistance. The towns were occupied. The heretics were burned. The greatest nobles were sent to the block or driven, like William of Orange, from the country. The Netherlands lay at Philip's feet; and Alva's army lowered like a thundercloud over the Protestant West.

The triumph of Catholicism and the presence of a Catholic army in a country so closely connected with England at once revived the dreams of a Catholic rising against Elizabeth's throne, while the news of Alva's massacres stirred in every one of her Protestant subjects a thirst for revenge which it was hard to hold in check. Yet to strike a blow at Alva was impossible. Antwerp was the great mart of English trade, and a stoppage of the trade with Flanders, such as war must bring about, would have broken half the merchants in London. Elizabeth could only look on while the Duke trod resistance and heresy under foot, and prepared in the Low Countries a securer starting-point for his attack on Protestantism in the West, With Elizabeth indeed or her cautious and moderate Lutheranism Philip had as yet little will to meddle, however hotly Rome might urge him to attack her. He knew that the Calvinism of the Netherlands looked for support to the Calvinism of France; and as soon as Alva's work was done in the Low Countries the Duke had orders to aid the Guises in assailing the Huguenots. But the terror of the Huguenots precipitated the strife, and while Alva was still busy with attacks from the patriots under the princes of the house of Orange a fresh rising in France woke the civil war at the close of 1567. Catharine lulled this strife for the moment by a new edict of toleration; but the presence of Alva was stirring hopes and fears in other lands than France. Between Mary Stuart and the lords who had imprisoned her in Lochleven reconciliation was impossible. Elizabeth, once lightened of her dread from Mary, would have been content with a restoration of Murray's actual supremacy. Already alarmed by Calvinistic revolt against monarchy in France, she was still more alarmed by the success of Calvinistic revolt against monarchy in Scotland; and the presence of Alva in the Netherlands made her anxious above all to settle the troubles in the north and to devise some terms of reconciliation between Mary and her subjects. But it was in vain that she demanded the release of the Queen. The Scotch Protestants, with Knox at their head, called loudly for Mary's death as a murderess. If the lords shrank from such extremities, they had no mind to set her free and to risk their heads for Elizabeth's pleasure. As the price of her life they forced Mary to resign her crown in favor of her child, and to name Murray, who was now returning from France, as regent during his minority. In July, 1567, the babe was solemnly crowned as James the Sixth.

But Mary had only consented to abdicate because she felt sure of escape. With an infant king the regency of Murray promised to be a virtual sovereignty; and the old factions of Scotland woke again into life. The house of Hamilton, which stood next in succession to the throne, became the centre of a secret league which gathered to it the nobles and prelates who longed for the re-establishment of Catholicism, and who saw in Alva's triumph a pledge of their own. The regent's difficulties were doubled by the policy of Elizabeth. Her wrath at the revolt of subjects against their Queen, her anxiety that "by this example none of her own be encouraged," only grew with the disregard of her protests and threats. In spite of Cecil she refused to recognize Murray's government, renewed her demands for the Queen's release, and encouraged the Hamiltons in their designs of freeing her. She was in fact stirred by more fears than her dread of Calvinism and of Calvinistic liberty. Philip's triumph in the Netherlands and the presence of his army across the sea was filling the Catholics of the northern counties with new hopes, and scaring Elizabeth from any joint action with the Scotch Calvinists which might call the Spanish forces over sea. She even stooped to guard against any possible projects of Philip by fresh negotiations for a marriage with one of the Austrian archdukes. But the negotiations proved as fruitless as before, while Scotland moved boldly forward in its new career. A Parliament which assembled at the opening of 1568 confirmed the deposition of the Queen, and made Catholic worship punishable with the pain of death. The triumph of Calvinistic bigotry only hastened the outbreak which had long been preparing, and at the beginning of May an escape of Mary from her prison was a signal for civil war. Five days later six thousand men gathered round her at Hamilton, and Argyle joined the Catholic lords who rallied to her banner. The news found different welcomes at the English court. Elizabeth at once offered to arbitrate between Mary and her subjects. Cecil, on the other hand, pressed Murray to strike quick and hard. But the regent needed little pressing. Surprised as he was, Murray was quickly in arms; and cutting off Mary's force as it moved on Dumbarton, he brought it to battle at Langside on the Clyde on the thirteenth of May, and broke it in a panic stricken rout. Mary herself, after a fruitless effort to reach Dumbarton, fled southward to find a refuge in Galloway. A ride of ninety miles brought her to the Solway, but she found her friends wavering in her support and ready to purchase pardon from Murray by surrendering her into the regent's hands. From that moment she abandoned all hope from Scotland. She believed that Elizabeth would in the interests of monarchy restore her to the throne; and changing her designs with the rapidity of genius, she pushed in a light boat across the Solway, and was safe before the evening fell in the castle of Carlisle.

The presence of Alva in Flanders was a far less peril than the presence of Mary in Carlisle. To restore her, as she demanded, by force of arms was impossible. If Elizabeth was zealous for the cause of monarchy, she had no mind to crush the nobles who had given her security against her rival simply to seat that rival triumphantly on the throne. On the other hand to retain her in England was to furnish a centre for revolt. Mary herself indeed threatened that "if they kept her prisoner they should have enough to do with her." If the Queen would not aid in her restoration to the throne, she demanded a free passage to France. But compliance with such a request would have given the Guises a terrible weapon against Elizabeth and have insured French intervention in Scotland. For a while Elizabeth hoped to bring Murray to receive Mary back peaceably as Queen. But the regent refused to sacrifice himself and the realm to Elizabeth's policy. When the Duke of Norfolk with other commissioners appeared at York to hold a formal inquiry into Mary's conduct with a view to her restoration, Murray openly charged the Queen with a share in the murder of her husband, and he produced letters from her to Bothwell, which if genuine substantiated the charge. Till Mary was cleared of guilt, Murray would hear nothing of her return, and Mary refused to submit to such a trial as would clear her. So eager however was Elizabeth to get rid of the pressing peril of her presence in England that Mary's refusal to submit to any trial only drove her to fresh devices for her restoration. She urged upon Murray the suppression of the graver charges, and upon Mary the leaving Murray in actual possession of the royal power as the price of her return. Neither however would listen to terms which sacrificed both to Elizabeth's self-interest. The Regent persisted in charging the Queen with murder and adultery. Mary refused either to answer or to abdicate in favor of her infant son.