For the moment England was saved, but the ruin of Mary's hopes had not come one instant too soon. The great conflict between the two religions, which had begun in France, was slowly widening into a general struggle over the whole face of Europe. For four years the balanced policy of Catharine of Medicis had wrested a truce from both Catholics and Huguenots, but Condé and the Guises again rose in arms, each side eager to find its profit in the new troubles which now broke out in Flanders. For the long persecution of the Protestants there, and the unscrupulous invasion of the constitutional liberties of the Provinces by Philip of Spain, had at last stirred the Netherlands to revolt; and the insurrection was seized by Philip as a pretext for dealing a blow he had long meditated at the growing heresy of this portion of his dominions. At the moment when Mary entered Lochleven, the Duke of Alva was starting with an army of ten thousand men on his march to the Low Countries; and with his easy triumph over their insurgent forces began the terrible series of outrages and massacres which have made his name infamous in history.

No event could be more embarrassing to Elizabeth than the arrival of Alva in Flanders., His extirpation of heresy there would prove the prelude for his co-operation with the Guises in the extirpation of heresy in France. Without counting, too, this future danger, 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 her 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, for Antwerp was the great mart of English trade, and a stoppage of the trade with Flanders, such as war would bring about, would have broken half the merchants in London. Every day was deepening the perplexities of Elizabeth, when Mary succeeded in making her escape from Lochleven. Defeated at Langside, where the energy of Murray promptly crushed the rising of the Catholic nobles in her support, she abandoned all hope of Scotland; and changing her designs with the rapidity of genius, she pushed in a light boat across the Solway, and was safe before 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 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." Her ostensible demand was for English aid in her restoration to the throne, or for a free passage to France: but compliance with the last request would have given the Guises a terrible weapon against Elizabeth and have ensured a new French intervention in Scotland, while to restore her by arms to the crown she had lost was impossible.

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, while Mary refused either to answer or to abdicate in favour of her infant son. The triumph indeed of her bold policy was best advanced, as the Queen of Scots had no doubt foreseen, by simple inaction. Her misfortunes, her resolute denials, were gradually wiping away the stain of her guilt, and winning back the Catholics of England to her cause. Elizabeth "had the wolf by the ears," while the fierce contest which Alva's presence roused in the Netherlands and in France was firing the temper of the two great parties in England.

In the Court, as in the country, the forces of progress and of resistance stood at last in sharp and declared opposition to each other. Cecil at the head of the Protestants demanded a general alliance with the Protestant churches throughout Europe, a war in the Low Countries against Alva, and the unconditional surrender of Mary to her Scotch subjects for the punishment she deserved. The Catholics on the other hand, backed by the mass of the Conservative party with the Duke of Norfolk at its head, and supported by the wealthier merchants who dreaded the ruin of the Flemish trade, were as earnest in demanding the dismissal of Cecil and the Protestants from the council-board, a steady peace with Spain, and, though less openly, a recognition of Mary's succession. Elizabeth was driven to temporize as before. She refused Cecil's counsels; but she sent money and arms to Condé, and hampered Alva by seizing treasure on its way to him, and by pushing the quarrel even to a temporary embargo on shipping either side the sea. She refused the counsels of Norfolk; but she would hear nothing of a declaration of war, or give any judgement on the charges against the Scottish Queen, or recognize the accession of James in her stead.

The effect of Mary's presence in England was seen in conspiracies of Norfolk with the Northern Earls and with Spain. Elizabeth, roused to her danger, struck quick and hard. Mary Stuart was given in charge to Lord Huntingdon. Arundel, Pembroke, and Lumley were secured, and Norfolk sent to the Tower. But the disasters of the Huguenots in France, and the news brought by a papal envoy that a Bull of Deposition against Elizabeth was ready at Rome, goaded the great Catholic lords to action, and brought about the rising of the houses of Neville and of Percy. The entry of the Earls of Northumberland and Westmoreland into Durham proved the signal for revolt. The Bible and Prayer-book were torn to pieces, and Mass said once more at the altar of Durham Cathedral, before the Earls pushed onto Doncaster with an army which soon swelled to thousands of men. Their cry was "to reduce all causes of religion to the old custom and usage;" and the Earl of Sussex, her general in the north, wrote frankly to Elizabeth that "there were not ten gentlemen in Yorkshire that did allow [approve] her proceedings in the cause of religion." But he was as loyal as he was frank, and held York stoutly while the Queen ordered Mary's hasty removal to a new prison at Coventry. The storm however broke as rapidly as it had gathered.