The Turmoil, 1573-1603
The last thirty years of Elizabeth's reign are known today as the Turmoil. The word reflects both the extreme difficulties faced by Elizabeth and the complexity of their causes. There is only space here to give the barest of outlines of both these and their consequences.
Religion:
England's North American colonies (dark brown), showing the predominate religious position of the inhabitants, 1571:
Prior to Mary's death in 1558, it was widely believed that the new Queen was an avowed Protestant, and would restore the Crown's supremacy over the Church. In the event, however, this was not what happened. It is rather simplistic to say the Elizabeth had converted to Catholicism - indeed, her personal religious beliefs are a matter for debate to this day. The most likely explanation is that Elizabeth believed that she was taking a middle way: while staying nominally loyal to Toledo (if nothing else to avoid a war with Spain), she ended the inquisition instituted by her half-sister, and declared freedom of worship for both Catholics and Protestants.
This policy of toleration was initially a success - in the 1560s, Catholics and Protestants lived peacefully side by side. In fact, despite widespread grumbling (Elizabeth's moniker of 'the Heretic' was adopted by Catholics and Protestants alike, each feeling that she was on the opposite side of the religious divide), there was no widespread unrest in England itself for the duration of Elizabeth's reign. However in the rest of her territory religious issues only added to local grievances. In the 1570s the parishes of England's northern colonies broke away from the Anglican Church, and angry mobs started appearing, burning down the houses of 'Papists' and lynching Catholic priests, a phenomenon which soon spread to England's southern colonies. In Scotland an organised independence movement gathered momentum in the 1580s, chiefly with the aim of establishing a Presbyterian kingdom, and in Germany, assemblies of leading nobles openly debated whether it was better to be under the thumb of the Pope in Toledo or the Pope in Rome. Elizabeth did finally break from Toledo in 1602, but by then the move was greeted with cynicism by Protestants and outrage among Catholics - the Crown's religious authority had been irreperably damaged.
Wars:
For the first half of Elizabeth's reign, England was a country almost permanently at war. In part, this was due to Elizabeth's efforts to hold together her Grand Alliance, containing both Venice and Russia, though in thinking that her allies would help against Helvetia she was gravely mistaken. More important were England's incompetent attempts to pacify the native tribes of North America. English forces were woefully inadequate, leading to long, festering conflicts in which both Indians and local militia committed countless atrocities against the women and children on the other side, and at times the Indians held sway over large parts of New England and Quebec. By the 1570s, ordinary English, especially in the colonies, felt that the Queen could not or would not protect them, and increasingly formed their own armed forces, often simply for the purpose of taking revenge on the natives. These militiamen would soon play a crucial role in turning the religious violence into an armed struggle against the Crown.
The Swiss:
While the Turmoil would certainly have happened anyway, it seems likely that Elizabeth would have eventually been able to restore order to the provinces by force, had Helvetia not decided to intervene. In 1584 Helvetia invaded English holdings in North America, marking the start of a long series of conflicts with England.
The Confederation's official reason for war was 'to protect the religious freedoms of the colonists'. This had some justification - without a strong Protestant nation to defend them, the Protestants in America had called for Swiss support, and the defection of the Protestant enclave of Wilmington to the Swiss in 1583 increased the feeling within the Confederation that they would be seen as friends of the colonists. Certainly Henri de Navarre believed this, encouraging Huguenots under Swiss rule to end their resistance and declaring war on England a few years later.
However, the real motivator for the President was its fury at prime land in the New World, earmarked for future colonisation, being taken from it by the English. The rivalry between the two countries was plain to see by 1550, and some historians would argue that the wars were simply the natural conclusion of this. Indeed, the Swiss showed little interest in England itself, apart from in the first war, in which towns in Northern England and Wales were seized in order to cut England off from Scotland, in the hope that the rebellion there would succeed. By contrast the war in the colonies, Scotland and Germany was relentless, and it soon became clear to the locals that the Swiss had not come as liberators at all.