Actually there were more than two Jacobite Rebellions. Three major ones and at least one other (ie the 1719 rebellion) which didn't make such an impact. There was of course the 1715 and 1745 rebellions which are better known in England because they impacted on England but there was also the first Jacobite Rising which was 1689 where there were three battles in Scotland (Killiecrankie, Dunkeld and Cromdale) and of course the Battle of the Boyne in Ireland. There were some smaller ones which didn't get off the ground too.

In 1689 James lost his throne in England after he fled when William of Orange brought his army across. The Scottish Parliament reconvened (James had been ruthlessly suppressing the Presbyterians/Covenanters) and the Presbyterians reasserted their dominance. Both William&Mary and James were asked to present their cases as to why they should be monarch of Scotland. William's was conciliatory whilst James just claimed divine right etc and questioned the parliament's authority to ask such a question. So James was stripped of his throne and proclaimed a traitor. Viscount Dundee was his only significant supporter in parliament and so stormed out to head for the Highlands to start the 89 rebellion. In truth he had no choice as he was the chief henchman of James during the Killing Times etc so his cards would have been marked anyway. Dundee was killed at Killiecrankie though the Jacobites won that initial battle.