Tyler, Amy, and Emily were three regular trainers dragged into the third battle against the evil group Cipher and their Shadow Pokemon. And they were able to defeat them... At a high price. With one of his Pokemon partially corrupted by a new type of Shadow Energy, and the sting of betrayal fresh on his mind, Tyler wasn't in the greatest of positions. And then Arceus decided to enact a mass exodus... Now in an unknown world and an unknown body, they must learn to live with these ponies and find a cure to the shadows within.
Side story to zeusdemigod131's A New World, A New Way. This story will be using concepts and characters from Pokemon Colosseum and Pokemon XD: Gale of Darkness, including Wes, Rui, Michael, Shadow Pokemon, Cipher, and Snag Machines. Links here and here.