It's been three years since the end of the Distonian War, where humanity fought against the Disas Beasts. War Hero Otori Asuka has quit her job as a magical girl and gone back to being a regular high school student. But one day terrorists attack her city...

Asuka transformed into a magical girl again and protected her friend from the terrorists. Now, she hears information about Kurumi, another member of the Magical Five. Kurumi continues to fight.

Asuka and the others go to the pool to welcome Kurumi, the new transfer student. Asuka is enjoying her peaceful days, and her time as a magical girl seems like it ended many years ago, but...

Nozomi is kidnapped and tortured by Abigail and her allies. Asuka is worried when she hears that Nozomi's been kidnapped, but neither Public Safety nor M Squad can intervene...

As Kurumi escapes with Nozomi, Asuka fights the two Russian mercenaries. M Squad arrives to join the fight, but they lack any magic of their own...

Asuka's first mission after joining M Squad is to fight the Russian Mafia in Hokkaido. She learns that Tamara, another member of the Magical Five, may there be there as well...

Chisato Yonamine is an abused girl in Okinawa. One day, a member of the Babel Brigade recruits her to be a magical girl. Meanwhile, Asuka and her friends are heading to Okinawa.

As 6th Naha approaches, General Tabira, a powerful general from the Spirit World, appears from the other side of the Topology Bridge. But the Babel Brigade is after her too...

Asuka's friends are caught up in the battle with the Disas in Okinawa. Mia and Tamara fight on the front lines. As many soldiers die, Asuka and Kurumi's battle is about to begin.

Kurumi battles Chisato as Asuka battles Geese. As Geese deploys his anti-Magical Girl weapons, it's Izuka who takes action.

The battle at 6th Naha is over, and Asuka remembers the words of the Magical Girls from the battle three years ago. "When this attle is over..." Magical Girl Asuka's answer is...