The three brothers discover that the human experiment banned after destroying the "Orochi", is still going on to secretly revive the evil snake. They also find out that some ex-members of the Yamainu (the Japanese military unit formed to kill the snake) are behind this conspiracy. The brothers fight together again in a battle against the military.
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.
