In this world, Sensha-do (戦車道), the art of tank-combat, is a traditional Japanese martial art for girls. Miho, a girl who just transferred into the Ōrai Girls' Academy in Ibaraki Prefecture, has been ordered by the academy's student council chairperson to join the school team and compete in the national Sensha-do championships.

In a futuristic society, Japan has implemented a complex system referred to as "The Red Threads of Science" to encourage successful marriages and combat increasingly low birthrates. Based on a compatibility calculation, young people at the age of 16 are assigned marriage partners by the government, with severe repercussions awaiting those who disobey the arrangement. For Yukari Nejima, a teen that considers himself average in every way, this system might be his best shot at living a fulfilling life.

In a brutal war between devils, hunters, and secret enemies, a mysterious girl named Reze has stepped into Denji's world, and he faces his deadliest battle yet, fueled by love in a world where survival knows no rules.

Following Madoka's rewriting of the universe, sacrificing herself and her happy normal days to save all magical girls from the cruel fate that awaited them by wiping witches out of existence, the despair still manifest into creatures known as nightmares. Magical girl Homura Akemi continues to fight alone in the hope that she will be able to see Madoka smile again.

She has a loving family and best friends, laughs and cries from time to time... Madoka Kaname, an eighth grader of Mitakihara middle school, is one of those who lives such a life. One day, she had a very magical encounter. She doesn't know if it happened by chance or by fate yet. This is a fateful encounter that can change her destiny. This is a beginning of the new story of the magical witch girls.