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.

As the young girls have discovered the truth about the cruel fate of a magical girl, one magical girl after another is destroyed. Throughout it all, there is one magical girl who continues to fight alone - Homura Akemi. Puella Magi Madoka Magica the Movie Part II: Eternal is a retelling of the second half of the TV anime series.

Madoka Kaname, an ordinary middle-schooler, along with her best friend Sayaka Miki, are offered the chance to have any wish they want granted by the mysterious Kyubey, and become magical girls and fight witches. However, fellow magical girl Homura Akemi seems intent on stopping Madoka from becoming a magical girl at any cost. Puella Magi Madoka Magica the Movie Part I: Beginnings is a retelling of the first half of the TV anime series.

June 1998: After spending two years in a coma caused by a traffic accident, Shiki Ryougi awakens with amnesia. She is visited by Touko Aozaki, a wizard and proprietor of a studio called Garan no Dou. Shiki has lost not only the memory of her accident, but also any real sense that she's even alive. Strangely, enigmatic beings begin to attack her...

Tomoe Enjou is attacked by bullies from his old school and saved by Shiki Ryougi. He asks her to hide him at her place and admits that he killed someone. Several days later, there are still no broadcasts about the murder as if it didn't happen... and when the victims are found, they're alive and unharmed.

After being branded a potential threat by the hero village, Basara returns home with his companions, where their bonds deepen amid growing tension over a summons to face the elders. Encouraged by Chisato and strengthened by his friends, Basara overcomes a trial that forces him to confront his doubts and accept that he doesn’t have to fight alone. United in resolve, the group sets out together for the hero village, ready to face what lies ahead.