After the events of Skyward Sword, changes soon start coming to Skyloft as well as the Surface.
People from neighboring islands come to Skyloft making Link and Zelda's former home the battlefield for the great mechanical revolution bent on ending the Loftwing way of life.
The four sacred dragons have begun fighting, creating unusual and dangerous happenings on the surface. Link and the Knights from the Academy traverse between the surface and the sky to try and find balance between the two and rise a new community below.
But there are greater forces at work, forces greater than Link, or even Zelda can comprehend...