Shortly after the Inter-High of Kagami and Kuroko's second-year, a street basketball team from the USA called Team Jabberwock came to Japan to play a friendly match against a Japanese college-level street basketball team, Team Strky. Despite their best efforts, Strky is brutally crushed by Jabberwock. After the match, the Jabberwock players insult the players from Strky and all of Japanese basketball, claiming Strky's basketball was at the same level as monkeys and telling the players and crowds to quit playing basketball and kill themselves. As a revenge match, Kagetora assembles a dream team of all members of Generation of Miracles plus Kuroko Tetsuya and Kagami Taiga, along with bench players Hyūga Junpei, Takao Kazunari, and Wakamatsu Kōsuke, forming Team Vorpal Swords, with the hopes of reclaiming the pride of Japanese basketball.

In the story, Kagami Taiga has just enrolled into Seirin High School when he meets Kuroko Tetsuya of the school's basketball team. Kuroko happens to be the shadowy sixth member of the legendary Generation of Miracles basketball team. Together, Kagami and Kuroko aim to take their team to the inter-high school championship - against Kuroko's former teammates.

Kasugano Haruka and his sister Sora have lost both their parents in an accident, and with them all their support. They decide to move out of the city to the rural town where they once spent summers with their late grandfather. At first everything seems familiar and peaceful, but changes come as Haruka starts to remember things from his youth.

Tsubomi Hanasaki is a girl in the second grade of middle school who likes flowers and plants. One day she experiences a weird dream. In that dream, a large blooming tree appears. Suddenly it is losing all of its flowers and a fairy appears. A few days later after Tsubomi has transferred to Meidou Gakuen, suddenly the fairy from the dream appears before her and pleads to Tsubomi to become the legendary warrior Precure and protect the Heart Tree. However, Tsubomi declines as she doesn't think that she would be able to do that. However, a mysterious enemy suddenly strikes and steals the heartflower of Erika Kurumi, Tsubomi's new classmate. Now she doesn't have a choice. To retrieve Erika's heartflower she has to transform into Precure and fight. Working up the courage Tsubomi turns into Cure Blossom and a new chapter of Pretty Cure begins!