The Legend of Zelda: Goddess of Wisdom
The Legend of Zelda: Goddess of Wisdom was released in 2010 and is an unofficial game in the Legend of Zelda series.
Goddess of Wisdom features an entirely new story and seems to be set in a different timeline which has provided the developers with a lot of freedom for the plot. The game begins with Link's Uncle racing to save Princess Zelda who was captured by the Council of Wizards; as expected, things go awry, and Link must save Zelda himself.
As the game continues, it becomes clear why the Council kidnapped Zelda and Link is the only one who can save the world from the horror that's about to be unleashed. The Wizards have also stolen the Crystal of Wisdom shattered it and spread the pieces to their members in preparation for their plans to pass. It's a classic Legend of Zelda style story and considering the Council of Wizards is looking to take over the world, it's not surprising that Ganondorf is somehow involved.