Approximately 6 months after the conclusion of the VF Circuit, Aichi Sendou transfers to Miyaji Academy to attend high school. After he meets Naoki Ishida and Kourin Tatsunagi transfers to his class, Aichi decides to establish a Cardfight!! Vanguard club at the school. Shingo Komoi and Misaki Tokura also join the club. However, the Student Council consider the Vanguard Club to be a disruptive influence in the school and oppose its existence.

In between a High School Circuit and the reintroduction of old friends and rivals, a new force emerges that seeks to take over Earth and Cray.