One hundred years ago, the desert city "Désser City" got severely damaged in a battle between Pokémon. The battle was started due to one specific Pokémon.
However, the Pokémon got sealed by someone, and the city went back to being as peaceful as ever, a state it still is in today.

As Satoshi, Pikachu and the others continue their journey, they encounter the mythical Pokémon Hoopa, who carries "rings that can summon anything and everything", and a girl named Mary who takes care of Hoopa.

The mischievous Hoopa starts summoning all kinds of things from its rings, including its favorite food, donuts, to everyone's surprise and enjoyment.
Ever a prankster, the simple-minded and innocent Hoopa starts referring to Satoshi and Pikachu as "Saton" and "Pikan". It quickly befriends the group, and they all decid to travel together.

Once they arrive in Désser City, Satoshi and the others meet Mary's older brother, Barza.
However, something seems off about him. On a closer look, he's holding the "Prison Bottle" that's said to have sealed the Pokémon that once destroyed the city!

An evil air drifts out of the bottle. It appears that the seal has become undone over all this time.
Just then, legendary Pokémon giving off that same air appear! Primal Groudon, Primal Kyogre, Dialga, Palkia, Giratina and Kyurem... This will put the city in extreme danger.

In order to protect the city, Hoopa makes more legendary Pokémon "Appear!" from its rings! Will Satoshi and his friends manage to protect Désser City alongside the legendary Pokémon Hoopa made "Appear!"? And what is the true identity of this evil power?

LEGEND VS LEGEND!
The most fierce battle in Pokémon movie history is about to begin!