Cobra, a notorious space pirate, is enlisted by bounty hunter Jane to rescue her sister from the strange being known as Crystal Boy, but then finds himself drawn into a complex struggle over the fate of a mysterious wandering planet.

(Source: ANN)

The film's plot tells the story of how Satoshi and Pikachu came to know each other. Pikachu was not cooperative toward Satoshi, but Satoshi only wanted to be friends with Pikachu. On the day they set out from Masara Town, both of them saw a Ho-Oh flying and made a vow to someday go and meet it.

(Source: ANN, edited)

After participating in the Johto League, Satoshi decides to begin anew in yet another journey; this time by himself and Pikachu, in the land of Houen. Though he isn't alone for long, as 10-year-old Haruka (whom dislikes Pokemon, but just wants to come along to see the world) travels with him after Pikachu destroys her bicycle. Satoshi also meets up with his old companion, Takeshi, and Haruka's younger brother, Masato. Together, they travel along in Houen, battling Gym Leaders, entering Contests, and other events on the way to the Houen League. (Source: ANN, edited)

Zenigata arrives on the ship "Machine Gun Kelly", a casino on the water owned by the mafia, because Lupin plans on stealing the casino's money. Lupin and his gang manages to break into the ship's vault but was unable to escape with the money due to Zenigata's shooting. However, there was another purpose the ship had, one that Lupin was aware of; to search for a sunken ship filled with gold. Lupin managed to steal this data while he was on the ship, however, now they have to contend with Zenigata, the mafia, and a secret organization whose base is under Alcatraz, as they attempt to uncover the secret behind the organization and the sunken treasure.

(Source: ANN)