Two years after the battle against Eosmon, Davis Motomiya, Ken Ichijouji, Yolei Inoue, Cody Hida, T.K. Takaishi, and Kari Kamiya meet a boy named Rui Owada, who is found with a depowered Digivice and claims to be the first Digidestined ever. In addition, a Digimon named Ukkomon appears in the real world, who wants every person in the world to have their own Digimon partner.

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.