It is made extremely clear however, the large extent to which politics influenced the settlement, because the Church established was more Catholic than Elizabeth had originally intended. The Parliament had pressured Elizabeth to make the Protestant Church more Catholic, to be acceptable to the majority of the country (avoiding civil wars and rebellion) and to guarantee Catholic international partners that little had changed, ensuring political pacts to remain intact. Elizabeth was also pushed to compromise with Catholicism to satisfy the House of Lords – even changing her title to the 'Supreme Governor" of the Church, instead of "Head" of Church, as she was a woman. C. Haigh states, "The Queen's tactics had been designed to contain conservative opposition in the Lords" Elizabeth made concessions to Catholics, and exhibited religious tolerance towards them – not punishing them as long as they were outwardly obedient – to not arouse animosity. In doing this, she allowed English Catholics to practice "dual loyalty," where they stayed loyal to both their religion and the Queen (by being externally submissive to her.) The 1559 Religious Settlement was an important cause as it provided the religious context for Mary's imprisonment – it made her a Catholic threat to the now Protestant England.
The medium-term cause of Mary's imprisonment was Mary's return from France to Scotland in 1561, and claim to the English throne – indicating Mary's political ambitions. Mary Stuart, Queen of Scotland and Queen consort of France (through her marriage to Francis II), Elizabeth's cousin, returned to Scotland following the death of her husband. While Mary can be viewed as an international force, as she was the monarch of Scotland, and previously ruled as monarch of France, she immediately expressed her political intentions by attempting to reassert her claim to the English throne – showing the predominance of the political factor.
