Mary was next married to Lord Henry Darnley an English Catholic cousin of Mary who also had a claim to the English throne. This outraged Elizabeth as their combined claim to the throne increased the support that they would have for trying to depose her. There was very little Elizabeth could do about their marriage and Darnley in fact posed very little threat to Elizabeth's safety. In 15 Mary's husband Lord Darnley was murdered. Mary was thought to have been involved with his death along with another man, Bothwell. Bothwell and Mary had been close for some time and despite a public outrage against him following Darnley's murder, Mary married him a short time after. This angered the Scottish public greatly who then called for her to be deposed of the throne. In 15 Mary was taken prisoner and forced to abdicate the Scottish throne. She escaped to England where Elizabeth had her imprisoned. It was when she came to England that the threat to Elizabeth was at its greatest. Mary became the focus for everyone who did not like Elizabeth and wanted someone else on the throne.
This increased threat first became obvious in 1569 shortly after Mary had escaped to England. There was a rebellion in Northern England by Catholics who planned to overthrow Elizabeth and put Mary on the throne in order to make England Catholic again. Elizabeth sent an army that crushed the rebellion and although Mary supposedly did not agree with the rebellion she was not in a position to agree with it and her being in the county provided a focus for the rebels.
In 1569 the Duke of Norfolk a rich powerful Catholic made planned to marry Mary. Mary didn't refuse his offer but because of her situation said she would only agree with Elizabeth's permission. Elizabeth refused to give permission because the marriage would have meant that Mary had many more influential supporters in England.
In 1570 the Pope excommunicated Elizabeth. Although this was completely out of Mary's control it increased the threat that she posed to Elizabeth as the Pope encouraged Catholics to disobey Elizabeth. This meant anyone could try and overthrow Elizabeth on Mary's behalf.
In 1572 the Huguenots (French protestants) were massacred in Paris on St Bartholomew's day by Catholics led by the Guise family. As these were Mary's relatives it gave people an impression about her toleration of Protestants if ever she became monarch.
In the mid 1570's Jesuit priests came to England to convert and provide secret Catholic masses. Before Mary had come to England there had been no way for Catholics to receive mass.
In 1583 Mary was involved in the Throckmorton Plot but there wasn't enough proof against her for Elizabeth to have her punished.
In 1584 William of Orange was assassinated, he was a Protestant leader in the Netherlands where there was a minority of Catholics. Although Mary was not directly involved Elizabeth would have been able to draw parallels with the situation.
In 1585 there was an outbreak of war with Spain. Elizabeth had been helping the protestant Netherlands to rebel against Philip of Spain. Elizabeth also found out that Spain was building an Armada to invade and convert the English. This increased Mary's threat to Elizabeth as Mary being a Catholic would have complete support from Spain and if Elizabeth executed Mary there would be an instant reaction from Spain.
Many people wanted Mary dead, but Elizabeth refused to execute her cousin and fellow monarch, and wouldn't release her elsewhere in Europe because her enemies were sure to kill her. Mary owed her life to Elizabeth, but still the relationship between the two Queens was difficult, perhaps more than it had ever been. Mary resented being kept a captive in England, and longed to be restored to the Scottish throne. Elizabeth's councillors urged her to have the Scottish Queen executed, but Elizabeth resisted them. It was not until the Babington plot of 1586 that she finally saw that she must execute Mary before Mary had her killed. There was also proof of Mary's involvement which under the bond of association meant that she was guilty of treason Elizabeth was hurt and angry that Mary had personally endorsed her murder, when for almost twenty years, she had protected Mary's life. Mary was put on trial, she was found guilty of treason, and condemned to death..
In conclusion Mary's biggest threat to Elizabeth was that she was her Catholic heir. It was common for heirs to the throne to overthrow the present ruler but this threat would not have been as great if Mary hadn't been Catholic. Her Catholicism made her an alternative ruler to Elizabeth and provided her with influential support in her plans to depose the queen. Elizabeth faced many problems due to the threat that Mary posed against her but overcame them all maintaining her position and her power.
