As Shinsei Inazuma Japan was about to have a match with Inazuma Legend Japan, a mysterious attack of a person and a swarm of robots interrupted, and another mysterious girl's power drove the world into another dimension. As the world of Inazuma Eleven Go and Danball Senki W met, the two teams must work together to find out what happened to their worlds.

The story takes place in the wintry land of Shantia, with Manatsu and the others invited to the land by its princess Sharon. But as they arrive, a mysterious monster attacks Shantia, and it is closed off to outsiders.

Star Driver takes place on the fictional Southern Cross Isle. One night, a boy named Takuto washes up on shore swimming from the mainland. He later enrolls in Southern Cross High School as a freshman and makes new friends.

Yorn gazes up at two massive cities floating in the sky and dreams of discovering their mysteries. Without warning, those mysteries come looking for him. Edenic assassins murder his father and Yorn is next on the hit list. A nameless old man and a mysterious young girl help Yorn on his quest to find his long-lost mother and the truth. Known as the God Hunter, Yorn leads a race against the dark designs of the technological overlords.