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Elizabeth's first policy towards Scotland was to oppose the French presence there. She feared that the French planned to invade England and put her Catholic cousin Mary, Queen of Scots, on the throne. In 1565 Mary married Henry Stuart, Lord Darnley, who carried his own claim to the English throne, but he quickly became unpopular and was murdered in February 1567 by conspirators almost certainly led by James Hepburn, 4th Earl of Bothwell. Mary married Bothwell, arousing suspicions that she had been party to the murder of her husband.

Rather than risk returning Mary to Scotland with an English army or sending her to France and the Catholic enemies of England, her cousin detained her in England, where she was imprisoned for the next nineteen years.

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https://www.elizabethi.org/contents/armada/speech.html

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The Protestant Elizabeth faced difficulties upon becoming Queen with regard to legitimacy, especially from  Catholics. This was due to the actions of her father, Henry VIII, in 1533. Many people refused to recognize Elizabeth as a legitimate heir because her mother was Anne Boleyn, who was Henry VIII’s second wife. The fact that the Pope never approved Henry VIII’s divorce from Catherine of Aragon in 1533  combined with the fact that Catherine was still alive when Elizabeth was born.
Another extremely important problem Elizabeth had to face were the threats from the Auld Alliance of France and Scotland, two Catholic countries   between England. What made the Auld Alliance stronger at this time was the fact that Mary, Queen of Scots was married to the French Prince Francis II. She, had declared herself the legitimate Queen of England (owing to the fact that she was Elizabeth’s second cousin and the granddaughter of Henry VIII’s sister Margaret) and she had the support of many English Catholics.