Giratina is the sole Pokémon living in the Reverse World, a little-known realm adjacent to our own. Enraged when Palkia and Dialga disrupt time and space, it drags Dialga into the Reverse World for a battle—but the conflict is broken up by a tiny Shaymin, the Gratitude Pokémon!

After departing the Reverse World and meeting Jiwoo and his friends, Shaymin—communicating telepathically—asks for help so it can be reunited with the other Shaymin in the Gracidea garden.

Soon after Jiwoo and his friends agree to assist Shaymin, they're dragged into the Reverse World and meet Muhan Graceland, who's been researching the mysterious realm. Little do they know that Muhan's former assistant, Zero, seeks to harness Giratina's power to rule the Reverse World, even if that means destroying the real world!

Can our heroes and their Pokémon thwart Zero's evil plans and protect both worlds? Will Giratina resolve its differences with Dialga? And what will Jiwoo and his friends learn about that special Shaymin?