Asuta Jimon, a runaway, is wandering the streets at night when he has a chance encounter with a young girl collapsed beside her tricycle. After he offers her some food, she is moved by his kindness and asks him to join her organization, offering him a face mask and a sweet bun. In need of a place to stay, Asuta decides to play along and accepts her offer, adopting the nickname "Dva." Little does Dva know, this cute girl is Kate Hoshimiya, the leader of Zvezda, a secret organization bent on world conquest. However, he soon realizes the true weight of her words as peculiar happenings rope him deeper into Zvezda and its eccentric members—the samurai-like vanguard Itsuka Shikabane, tech-genius Natalia "Natasha" Vasylchenko, troublesome Yasubee "Yasu" Morozumi, ex-gangster Gorou Shikabane, and multi-purpose robot Roboko Tsujii. With "White Light," a powerful organization of justice, and the entire Japanese government against them, can Zvezda really dominate all humanity and let their light shine throughout the world? [Written by MAL Rewrite]

A comet burns in the sky, its brilliant light shining down upon the people of Earth. At that time, a giant army of viruses invade the real world, crushing everything in their path. Netto and Enzan use cross fusion to intervene, but are whisked away to an unknown location, only to be confronted by the one responsible for the attack - Duo!

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)