Shadowverse Flame features a new protagonist Light Tenryu and its story is set in Shadovar College, a facility that trains professional players of the Shadowverse game. Tenryu Light, a transfer student, decides to join "Seventh Flame," one of the seven Shadovar clubs. However, Seventh Flame is on the verge of closure due to a lack of members! In order to avoid the club's demise, Light decides to look for new members. But what awaits him are powerful rivals who control a wide variety of cards...

After inheriting the company from their parents, siblings Yuuhi and Yuamu Oudou have started to work at Ultraterrestrial Trouble Solutions, an organization that hunts aliens. Although they have never encountered aliens before, Yuuhi is desperate to meet one as he believes that an alien has stolen his important item called the "Earthdamar." One day, while searching for extraterrestrial creatures, Yuuhi and Yuamu find a strange spot in the forest where many trees have fallen, forming a scenery similar to a crop circle. As they venture further, they discover a mysterious spaceship and enter it out of curiosity. To their surprise, they come across Yudias Velgear, an alien from the Velgear Star Cluster. As it turns out, Yudias is seeking to learn about Rush Duel—a card game popular among elementary school students—as he believes that it will save his home from a long war. With the siblings agreeing to teach Yudias about Rush Duel, they eventually realize that their first contact with an alien may not be a random coincidence.

The isolationist Akane Clan, composed of an all-girls body mainly consisting of young kunoichi in training, has a code to which they all must adhere: "As men are dangerous beings, interacting with them is forbidden." Kunoichi Tsubaki, the leader of the Dog Squad, is an excellent trainee with a promising future, but she has started to experience a strange feeling in her heart... whenever the subject of boys is brought up.