Who would have been the successor to Elizabeth l if she died of smallpox in 1562?

I'd wager Lady Margaret Douglas. She had two healthy sons, is English-born, close in blood to the preceding monarchs (precedent is big in Common Law, and the successions of John Lackland and Henry VI could be construed as precedents for proximity of blood playing a role in succession), had been semi-acknowledge as a junior royal heiress before (both by Henry VIII and Mary) and probably better considered by the court/public than the silly Franco-Scottish Queen, the remaining Grey girls or Margaret Clifford.

Her son's marriage to Mary of Scots would probably avert war with Scotland, while at the same time pave the way for Scottish absorption into England: Margaret would be followed by Henry (IX) Stuart, King of England and Scotland, who would be far less likely to put the kingdom's affairs in the hands of Spanish and/or Frenchmen than his wife.
 
Wikipedia claims Mary, Queen of Scots and Lady Catherine Grey as genealogical possibilities on that date (by two competing inheritance theories).
Don't know enough to be sure what is likely to happen in reality.
 
- Mary, Queen of Scots was the heir by primogeniture, but Catholic, foreign-born and pro-France.
- Margaret Douglas was the senior native-born heir by primogeniture, but Catholic and excluded from the succession by Henry VIII.
- Catherine Grey was the heir in accordance with the succession laws set down by Henry VIII and Protestant (although she seems to have informed the Spanish she would convert if they helped her). A prisoner in the Tower and involved in an unpleasant ?marriage? with Edward Seymour, by whom she had two ?illegitimate? sons.
- Mary Grey, sister of Catherine, is the heir if Catherine and her ?bastards? are set aside. She was deformed and unmarried, making it likely Catherine's son would succeed her.
- Margaret Clifford, Countess of Derby, is the heir according to Henry VIII's will if you consider the Grey sisters to have forfeited their rights by their "involvement" in their sister's usurpation of the throne. Protestant, married with two sons.

Closest male candidates would be Henry Stuart, Lord Darnley, or Henry Hastings, Earl of Huntingdon, the great-grandson of Margaret Plantagenet (next-in-line in the Yorkist succession after Elizabeth of York's descendants) and Henry Stafford, 2nd Duke of Buckingham (senior descendant of Edward III's youngest son Thomas of Woodstock), who was her cousin many times over.
 
Elizabeth's council is going to have two main requirements

A succession that is going to "stick" and a Protestant one ideally.

At the time it seems the council was largely fixed on Catherine Grey - despite her clandestine marriage -her advantage was that under statute she was the lawful heir.
The issue of her marriage could be solved with a simple 'surprise' witness and the overturning of the Archbishop's declaration it was invalid.

She offers one major advantage a male heir (she was pregnant with her second at the time of Elizabeth's smallpox) and a Protestant husband who was close to Cecil.

Ultra Catholics and some more moderates will probably opt for Mary Stuart and it is likely that Catherine is going to face some trouble on that front. Mary has an advantage she is the undoubted heir by primogeniture and she is single (her marriageability is going to shoot up the scale) and if she marries abroad then that means a new foreign enemy for Catherine I in London.

If Catherine's council moves quickly, learning the lessons of Northumberland's botched attempt to make Jane Grey Queen, then they should manage to get Margaret Douglas and her sons into a comfortable custody.

Hastings was the outsider and he himself was very keen to make it clear that he wasn't interested.
 
Margaret Douglas lived in Yorkshire at the time, which might be a problem. Very easy for her to slip into Scotland or across to the continent.
 
Possible butterfly.

If Catherine Grey is Queen, then MQoS is far less likely to flee to England in 1568. She might or might not have a better claim to the English throne than Elizabeth (depending on one's views as to the latter's legitimacy) but she unquestionably had a better hereditary right than Catherine, so can't possibly flee into her clutches.

So the 1569 rising (if not butterfliued away) takes place with MQoS at liberty, and with a Queen who lacks the prestige of the Tudors.
 
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