The world of Pokemon is now in a peaceful era under the protection of goddess Yggdrasil and the Hero/ine of Legend, a group of Pokemon who received the blessing from the god Arceus. However, the tide of destiny seemed to hate this world as the force of chaos had appeared and plagued the realm, and the cause of it was from the Hero/ine of Legend themselves!

The realm of Pokemon is falling into the chaos. The evil force had risen the corpse of evil Pokemon and they start to invade the land! With the heart of justice, a young Lucario and his friends decide to start their adventure to dispose all evilness. But as the adventure proceeds, they found that everything leads their heart and soul deeper into the evilness!

After 17 years since he left at the end of OoT, Link returns to Hyrule, which now is inhabited by human and Pokemon. Link, along with his new Pokemon friends, receives a new mission to complete the forgotten legend. But after time pass, Link and his friends discover that this legend has led to the end of the world!