The Glorious Revolution
When Charles II died, the throne of England passed to his brother, James. This worried those loyal to the Church of England, as James was Catholic. But as long as his protestant daughters Mary and Anne were heirs to the throne, they tolerated him. When his queen gave birth to a son (who would definitely be raised Catholic), the English people rebelled. James fled to France where he lived in exile, and his daughter Mary and her husband Prince William of the Netherlands are crowned.
Penn’s fortunes changed dramatically after James II is overthrown. Penn was accused of treason for his loyalty to deposed King James II. In 1690 he was placed in the Tower of London for several weeks, but was cleared of all charges. However, in 1691 the government issued yet another arrest warrant, but does not actually arrest Penn.