Deeply divided between a king and a queen, Scotland was a shambles. James VI had been just a year old when his mother was forced to abdicate, with Lord Moray as regent. Though the boy king was generally accepted, Elizabeth still refused to recognize his authority. But in 1571, when a plot by Mary Stuart’s followers to kidnap James ended in Moray’s killing, Elizabeth took great offense.

It enraged Elizabeth that she was distrusted north of the border, even though lies and false promises had always tainted her policy in Scotland. Now the queen took out her frustration (and reinforced the distrust) by sending militias to lay waste to an area of southern Scotland twenty miles deep from sea to sea, smashing every stone house, burning every hut, and killing every animal. Her next target was more significant: Edinburgh Castle, which fell after a bombardment lasting eleven days.

Elizabeth was still willing to restore Mary to her throne, but only on certain conditions – and in determining what they would be, Elizabeth was often out of all reason. She demanded that hostages be sent to London, that English garrisons be stationed at Dumbarton and Edinburgh and that the port of Leith be opened to English warships.

Meanwhile, the young Scottish king was becoming more of an annoyance to Elizabeth. Letters from his mother gave him the idea that she was being mistreated. Elizabeth also insisted that the prince, as she pointedly referred to James VI, should be educated in England. Other nations had designs on the boy king, too, particularly the Guise faction in France.

Mary’s letters to her “dear sister” Elizabeth persisted, promising a stupendous secret she could only reveal in person. Mary always believed that, face–to-face, she could bend Elizabeth to her will. Meanwhile, Mary wrote to Philip II, encouraging him to invade England, and once that was accomplished, to extract her son and bring him up in Spain.

News from the Spanish lands was mixed. For whatever reason, Philip II was overlooking the English provocations and had urged his governors in the Low Countries to treat Elizabeth with respect. William of Orange pressed his rebellion to free the Low Countries from Spanish control, beseeching Elizabeth for more men and money, but it went against her royalist principles to support him in his struggles to oust the Spanish. Philip seemed interested in some kind of appeasement and compromise in the Low Countries, but no terms would convince the Dutch to submit to Spanish rule now; that ship had sailed.

In France, skirmishes that erupted after the St. Bartholomew massacres had quieted down - a good thing that was not, in practical terms, good for Elizabeth. The French were armed and dangerous, and her treaty with Catherine was a dead letter.

Charles IX had died, and Anjou had taken the throne as Henri III, but a precarious situation was developing between the new king and his brother Francois, the Duke of Alençon. In view of his penchant for cross-dressing, Henri was not expected to sire an heir, making it likely that Francois would become king. But Henri treated Alençon precisely as his brother had treated him when he himself was next in line for the throne behind Charles IX. He set to devising a way to get his younger brother out of the country.

Alençon would not go away quietly. But he couldn’t be allowed to stay in France to be made a rallying point for rebels. The Low Countries beckoned, and he would find a welcome among the rebels there. He had nothing to lose by taking arms against his brother – in defeat, he would likely be spared; but if he won, he would be king. Alençon himself was not choosy on the subject of religion and had even been a Protestant briefly.

Many options were presented to Elizabeth for the partition of the Low Countries, but she resisted lending the weight of the English Crown to any of them. This might seem an odd stance, if only because history would eventually see Elizabeth as the grandmother of British imperialism. However, it neatly expressed Elizabeth’s own beliefs. “It may be thought simplicity in me that all this time of my reign I have not sought to advance my territories and enlarge my dominions; for opportunity hath served me to do it,” she said upon dissolving the Parliament of 1593. “And I must say, my mind was never to invade my neighbors, or usurp over any; I am contented to reign over mine own.”

One such option came when the rebels’ wealth was depleted, and it was proposed that the Low Countries be divided among France, Germany, and England. Elizabeth, who had more than once been offered sovereignty over the Low Countries, rejected the proposal.

Closer to home, Elizabeth was proud of the way England’s religious strife had seemingly ironed itself out. All of Europe was frankly amazed. The Catholic unrest had apparently dissipated. With only one exception, the few resistant bishops who remained were in jail. The priests offered only a token recalcitrance that had no real consequences. The communicants seemed unconcerned.

Elizabeth deserved credit for her skillful ability to “convert” the kingdom. She exploited people’s desire to support a new monarch and to compromise in the name of stability. It seemed unlikely that millions of people would so readily abandon their faith for another, but in fact they hadn’t. Everyone was supposed to be Protestant. Plenty weren’t, but the new religious order wasn’t being strictly enforced. No one paid a price for holding onto their belief; Catholics could worship discreetly without fear of persecution. Still, if the change had been softened, it was still change. “There is no getting away from the shame of that great defection,” as one thoughtful Jesuit put it.

Priests, as worn out and confused as their flocks, remained in the realm, but they were adrift without direct orders from their superiors or even their peers. England’s Catholics still mattered a great deal in the grand European political scheme – discussed, weighed and calculated in a dozen capitals – but from their perspective, they were lost and alone, forgotten by the Church in Rome and the Holy Father.

But Rome didn’t sit idle in defeat for long. The Council of Trent, held between 1545 and 1563, condemned Protestant heresy. Then in 1570, Rome excommunicated Elizabeth, which had little immediate effect but was still a powerful statement. Catholics had come to terms with the fact that the power and prestige of the Renaissance papacy – for good or for ill - were behind them, and the pope could no longer enforce his will, but they found strength in the decree, knowing that their brethren left in England needed help. One plan to provide it was that the Guise clan, under papal decree, should lead a French force into England to free Mary and depose Elizabeth. The distinction was that this undertaking would be on behalf of France, but would be carried out for the Catholic cause, giving Philip of Spain no excuse to interfere.

There were still influential Catholics in England, quite a few. Many were Jesuits, and all were English or Scottish to the bone. They tried to stay out of politics, but that was difficult to do. Even the simplest testament to the pope’s supremacy was considered treasonous.

But the queen was not interested in making martyrs. The official royal position was that no English subject during Elizabeth’s reign had ever been tortured or put to death, or even imprisoned for long periods, because of his or her religious beliefs. People were stretched on the rack for interrogation about crimes against the throne, while those who were hanged were executed not for being Catholic, but for committing treason in the name of their faith. No one was burned, as occurred during Mary’s reign. Still, the human cost had been real, and Elizabeth did not like it.