Prologue
It wasn't until the fifth of January, 1569, that Lord James Hamilton, Lord of Arran, received the letter explaining the crisis in Scotland. Mary, Queen of Scots, had been arrested, passed around from prison to prison, and was now in England, awaiting a trial. Her son, the infant Prince James VI, had been declared King in her absence. However, in December the child had passed away (i) under the regency of his uncle, James Stewart. Steward had subsequently declared himself James VII, King of Scots, and was fighting against the supporters of Queen Mary. Stewart's assumption of the throne negated Hamilton's own claim - when he gave up the regency, he'd been promised by Mary of Guise that if Mary (Queen of Scots) died without issue, he would sit upon the throne of Scots. If Mary was awaiting execution (ii) and her son had met his demise, Hamilton was rightfully the King of Scotland! It was absurd that Stewart could make a power play like that, with a lesser claim! Naturally, Lord Hamilton was infuriated at the news, suspecting foul play on the part of Stewart, as well as being cross that the oath he had made with Mary of Guise had been broken. Immediately he departed from his estates in France (where he had retired once Queen Mary originally announced her pregnancy with the late James VI), and began the journey back to his homeland. On the fourteenth of January he arrived in Aberdeen, where he met with a group of his supporters. Among them were his sons James and John. In a weeks time they would march on Edinburgh Castle, and in quick succession topple Stewart's fragile regime and crown Hamilton as King. Stewart was thrown in prison on suspicion of murder, where he would stay for three years before finally being hanged, quartered and drawn for tge crime of regicide (iii). That very day, on January 22, 1569, in a very touching ceremony, James Hamilton was crowned James VII, (iv) King of Scots. Thus ended the rule of the House of Stuart over Scotland, and so would begin the rule of the House of Hamilton, one of the longest reigning royal houses in Europe.
In September of 1569, Mary, Queen of Scots, formally signed away her claim on the throne of England (v), and since she could not return with an army of Scotsmen, Queen Elizabeth released her from custody. Mary however, did try to return to Scotland and regain power: in November she, with a group of Stuart loyalists, attempted a coup to push King James VII out of power. It failed miserably, with most of her faction drifting off. She was captured, and King James VII had her sign a similar agreement to the one she signed with Elizabeth, revoking her claim on the throne of Scotland - even though by all rights she was the true monarch of Scotland. He considered executing her, but in the end decided that would just weaken his own legibility as King of Scots. With Elizabeth in England, Hamilton in Scotland, and Catherine de Medici in France, Mary Stuart had no where to go. The former Queen of Scots took her fortunes and headed east, never to be seen again (vi). However, although beaten, bloodied, and thrown out of Scotland, history was not yet finished with the House of Stuart.
Afternotes
(i) The POD, is, of course, the death of James VI under the regency of James Stewart. He did not die at the hands of his uncle, as history books would say, but of fever.
(ii) Of course, no body truly knew that she would be executed, but as in OTL, once she was out of the picture she was rapidly forgotten about. Hamilton guessed that if Elizabeth had her hands on her, she was a goner. Poor Mary.
(iii) It was deemed fitting that an English puppet would die of an English execution style.
(iv) Technically, it would be James VIII, but he decided to forego the extra I - he refused to recognize James Stewart as a legitimate monarch.
(v) With her son dead and a new Dynasty in Scotland, Elizabeth sees Mary as less of a threat and merely has her sign away her claim and banished from England.
(iv) She did in fact, head east, to Milan, where a catholic woman could live in peace. She assumed the name of Mary Dunbar and passed herself off as the heiress to minor noble family back in Scotland. Eventually she married a Venetian merchant named Lorenzo. The two had four children and lived to the ripe ages of seventy (her) and seventy two (him). A much happier ending for someone who never really got to experience happiness.