The day before Queen Mary married the Duke of Norfolk in October 1567, she declared him to be King of Scotland. But she refused to grant him the crown matrlmonial, which would have given the rights of a king, independently of his relationship to her as Queen. It was the same with Lord Darnley.
Prince James was betrothed to Catherine Michelle (born 10 October 1567) the younger daughter of Elizabeth of Valois and Philip II of Spain. Elizabeth was the sister of Francis II of France, Mary's first husband and therefore her sister-in-law.
James Stewart, Earl of Moray, Mary's illegitimate half brother, was not murdered by a member of the Catholic Hamilton family. In OTL he was on 21 January 1570 because he was the Regent of James VI.
Pope Pius V excommunicated Queen Elizabeth in February 1570. The papal bull described Elizabeth as the pretended Queen of England. It released the Catholic faithful of England from any loyalty or obedience to her. It also threatened Catholics who remained loyal to Elizabeth with excommunication. All this was as in OTL.
The Ridolphi Plot was a plot by Roberto Ridophi, a Florentine banker and papal agent then living in London, in 1570 to 1571. It aimed to enlist a Spanish army to invade England in support of a rising of English Catholics, which would depose Elizabeth and put Mary on the throne of England.
Ridolphi travelled to the Netherlands where he met the Duke of Alba, Philip II's commander there. Alba poured cold water on Ridolphi's dreams. He would invade England only if Elizabeth was dead or at least held captive. Ridolphi then went to Rome. Pope Pius gave him moral support, but little else. From there he travelled to Madrid where he met King Philip. The Spanish king was enthusiastic about Ridolphi's plan and gave it his consent.
The Ridolphi plot was uncovered by the English government in April 1571. Mary knew about the plot. She wrote to Elizabeth, emphatically and truthfully declaring that she never consented to it. She swore by the child she was carrying in her womb, she was about five months pregnant, that she never gave the slightest approval to the plot. She addressed Elizabeth as her dear sister and professed her love and loyalty. . In OTL she was implicated in the plot. Mary gave birth to a son on 21 August 1571. She and her husband named him Robert.
The Saint Bartholomew Massacre of Protestants, Hugenots, in France took place on 23 and 24 August 1572. Tens of thousands were killed. Catherine de Medici, the Queen of France, was the mother of Franci s II, and Mary 's mother-in-law. She ordered the assasination of Coligny and other French Hugenot leaders.
Altnough Mary was a devout Catholic. she was not a fanatic nor a persecutor of heretics. As Queen she tolerated her Protestant subjects and accepted the reformed religion as the rwligion of Scotland. However she brought up her children in the Catholic faith. When she heard about the Massacre, she wrote to Elizabeth expressing her horror at the murder of so many innocent men, women and children.