Williamite War
James II was born Protestant, but converted to Catholicism in 1669. His deviant religion was no subject when King James II succeeded his brother King Charles II in 1685, but soon became a hot issue and triggered the Williamite War.

Although fought on Irish soil, the Williamite War was not an Irish war. In fact the Williamite War was an European battle brought to Ireland by King James II.
For the source of the conflict we have to go to Versailles. Despite treaties the Catholic French King Louis XIV reduced religious tolerance to the French Huguenots. He had also reorganised his army and conquered territory, such as the principality of Orange. The Protestant Prince of Orange, William, who was stadhouder (some sort of viceregent) of Holland at that time, led the fierce opposition against King Louis XIV.

William of Orange looked with Argus' eyes at the developments when the Catholic and French ally James II became king of England, Scotland and Ireland. William of Orange could not tolerate a second powerful enemy in Europe.

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King James II
Immediately after his coronation in 1685 King James II proclaimed a series of measurements aiming at the emancipation of Catholics, such as the Declaration of Indulgence. This, together with appointing Catholic officers, made him highly unpopular with the Parliament. As a result King James II simply abandoned the Parliament.
Without the ballast of the Parliament King James II replaced Protestants on military and political positions with loyal Catholics.
After the horrors of the Confederate War the royal support was welcomed by the Catholics on Ireland.

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William of Orange
At first Mary, the eldest daughter from King James' II marriage with Anne, was the successor to the throne. Because Mary was Protestant and King James II was well in his 50's at that time the Protestants initially decided to swallow and wait for better times. Their hope vanished when the second wife of King James II, Mary of Modena, gave birth to a son and a Catholic royal line was inevitable the Protestants took action.
Seven politicians asked their Protestant Dutch neighbour, William of Orange who was married with King James' II eldest daughter Mary, to take the crown and secure the Protestant line of the royal family.
William of Orange, not only eager to decrease Catholic influences, but also partially British by birth (son of Mary Stuart and grandson of King Charles I, in fact William and his wife were first cousins), accepted the invitation to overthrow his father-in-law King James II (nice family heuh?). An additional reason was perhaps that William of Orange was still pissed because King James II had captured the small Dutch trading post New Amsterdam a few years before and changed its name to New York.

An imposing Dutch fleet landed on 5 November 1688 at Brixham. William of Orange (King William III) and Mary II (Queen Mary) were declared sovereigns of England, Scotland and Ireland in January 1689. King Louis XIV immediately declared war to England and the Netherlands.