On the 5th November 1688 William, Prince of Orange landed at Torbay with an army of German mercenaries; whithin a matter of weeks, king James II had fled to France and the Glorious Revolution had begun. In the subsequent Bill of Rights 1689 parliament was to state that;
the said late King James the Second having abdicated the government and the throne being thereby vacant .... that William and Mary, prince and princess of Orange, be and be declared king and queen of England, France and Ireland and the dominions thereunto belonging
Despite this there were some that believed that James continued to be the rightful king of both England and Scotland until his death in 1701. These Jacobites as they were known, believed that kings were appointed by God to rule over nations, and that such divine appointments could not be overturned by mere acts of parliament. William and Mary were therefore mere usurpers, as indeed was Queen Anne and all the subsquent Hanoverian kings and all their descendants.
James II therefore remained the true king of England and an entirely separate Jacobite Succession of English (and Scottish) monarchs, marked what might be termed the alternative list of the Monarchs of England.
The Stuart 'Pretenders'
Although James made one serious attempt to regain his throne via Ireland and was famously defeated at the battle of the Boyne in 1690, he was to spend most of the rest of his life in exile as a pensioner of the king of France. After his death in 1701, his son by his second wife Mary of Modena, James Francis Edward Stuart, otherwise known as the Old Pretender, became James III of England and James VII of Scotland by the Jacobite reckoning, but there seemed very little chance of him ever being able to regain the throne.
The Act of Union 1707 that brought Scotland and England together as one United Kingdom was not universally welcomed; there was widespread opposition to the union within Scotland which found a focus and a potential rallying point in the form of the exiled James III. The cause of the restoration of the Stuart line therefore became inter-twined with notions of Scottish independence. There was an abortive Jacobite rising in Scotland in 1708 and a slightly more serious Jacobite Rebellion in 1715 when James III landed, but nothing much came of the affair and James rather lost interest after that point.
This James married Maria Clementina Sobieski, (the grand-daughter of the very Jan Sobieski who defeated the Turks) and the marriage produced two sons, the elder of which was named Charles, who in due course would become Charles III.
During his father's lifetime he was better known as the Young Pretender or Bonnie Prince Charlie as the Scots called him, With the promise of French support this Charles attempted to restore his father to the throne and landed in Scotland to encourage the Second Jacobite Rebellion of 1745. The '45 met some initial success, but ended in the bloody disaster of the battle of Culloden on the 17th January 1746. Although Bonnie Prince Charlie managed to escape death himself, he was a broken man thereafter, took to the bottle and eventually died in Italy in 1788.
Although Charles had a daughter by his mistress Clementina Walkinshaw, who was known as Charlotte Stuart, he had no legitimate children and on his death in 1788 the succession passed to his younger brother Henry IX. However the chances of Henry producing any offspring were somewhat remote as he had chosen a career in the Church and was a Cardinal at the time his brother died.
Apart from insisting that his staff now refer to him as 'His Majesty', the only practical step Henry IX took to secure the throne was limited to issuing a protest formally asserting his rights. Unsurprisingly, Henry was therefore the last of the Stuarts to lay claim to the thrones of England and Scotland, and it is at this point that most histories of the Jacobite cause come to an end.
Indeed the brutal suppression of Jacobite sympathisers after the failure of the '45 rather discouraged any further attempts at a Stuart restoration and Jacobitism became something of a romantic affectation, with its toasts to the king over the water and ceased to become of any practical consequence; but the Jacobite succession continued.
The House of Savoy
As far as the Cardinal Henry was concerned he was the rightful heir to the throne and on his death on the 13th July 1807, he bequeathed those rights to one Charles Emmanuel of Savoy. As it happens this Charles Emmanuel was not a random choice from amongst the crowned heads of Europe as he was in fact the great-great-grandson of Henrietta Anne Stuart, the youngest daughter of Charles I and therefore Cardinal Henry's closest living relative.
All the subsequent Jacobite 'claimants' to the throne of England base their claim on their descent from Henrietta Anne Stuart and her marriage to Philippe d' Orleans, the Duke of Orleans. Of course the supporters of the Glorious Revolution had already thought of this one, and by the Act of Succession 1702 had specifically excluded the descendants of the said Henrietta Anne Stuart from the succession.
In any event Charles Emanuel therefore became Charles IV by the Jacobite reckoning, although he is better known as Charles Emmanuel III and king of Sardinia, a position which he held until his death in 1819. On his death he had no legitimate offspring and so the succession passed to his brother Victor otherwise known as Victor Emmanuel I who was also King of Sardinia. On Victor's death in 1844 the succession passed to his eldest daughter Maria Beatrice who therefore became Mary III of England and Mary II of Scotland.
Apparently it is the tradition amongst Jacobites is to consider Mary Tudor as Mary I and Mary, Queen of Scots as Mary II of England (and of course Mary I of Scotland) and therefore Maria Beatrice of Savoy was Mary III of England etc.
The House of Habsburg-Lothringen
This Mary III or Maria Beatrice married Francis IV Archduke of Austria, who was of course a Habsburg, and so once Maria Beatrice had died in 1840, it was their eldest son Franz von Habsburg who duly became Francis I of both England and Scotland.
Francis I however died without issue at Vienna, on the 20th November 1875 after a thirty five year reign, and he was therefore succeeded by his niece, Maria Theresa. She was the daughter of his younger brother Ferdinand (who had predeceased Francis) and duly became Mary IV of England and Mary III of Scotland.
The House of Wittlesbach
Maria Theresa married the Prince and later King Ludwig of Bavaria, and lived until 1919, at which time the Jacobite succession passed to their eldest son. Although named Rupprecht, and hence normally Rupert in English the proper form of his name for regnal purposes is apparently 'Robert' and thus he appears as Robert I of England or Robert III of Scotland.
From Rupprecht von Wittlesbach the succession passed to his eldest son Albrecht von Wittlesbach or king Albert and subsequently to Albert's eldest son Francis, or to give him his full name Franz Bonaventura Adalbert Maria von Wittelsbach, who is currently, as Francis II, the true king of both England and Scotland. Our King Francis II, who styles himself as the Duke of Bavaria, speaks English, French, German, and Hungarian, survived a period of confinement at the concentration camps of Oranienburg and Dachau during his youth, and seems a thoroughly reasonable king who has devoted much of life to charitable and educational endeavours.
Although Francis II has no children himself, his younger brother, the Prince Max of Bavaria, who is the next in line, has five daughters and a number of grand and great-grandchildren, so their are at least 109 living individuals ready to take on the succession in due course.
Of course, none of the Jacobite successors from Charles Emmanuel onwards have made the slightest effort at recovering the throne, nor indeed have any of them ever indicated the slightest interest in doing so. (Although there are tales of Albert sporting the Stuart tartan from time to time.) But if ever the British public come to tire of the antics of the Schleswig-Holstein-Sonderburg-Glücksburg family, it may well be a comfort to them that there are some readymade alternatives at hand.
The Jacobite Succession
From 1688 to the Present Day
The first ordinal referred to above, designates the individual's position as king of England the second as king of Scotland, hence Henry is the ninth king of England to bear that name, but the first of Scotland.
Louise Yeoman The Jacobite Cause From the BBC History website
Noel S. McFerran The Jacobite Kings and Their Heirs