Ureshiko Asaba, 26 years old, married. Few people know the fact that she is a magical girl named "Agnes", and she is actually the guardian of the town where she lives. One day she meets Sayaka Kurenai, aka "Cruje", another magical girl appointed by the magic realm as the legitimate sucessor to her position, but Agnes is reluctant in letting her assume because she knows that Cruje has orders to erase the whole place, including its human inhabitants with the purpose of creating a new one. To complicate matters, Ureshiko must deal with the growing distance between her and her husband, Tamotsu, her crescent feelings for Tatsumi Kagura, a young man who is now living as a tenant in her home, and the fact that in the moment she ever kisses a common human, she would lose her powers forever.

The infamous series of unexplainable murders in Hinamizawa have been solved and the chains of fate have broken due to the efforts of Rika Furude and her friends. Rika believes she has finally obtained the normal and peaceful life she desired with her friends; however, she is proven wrong when the wheels of fate begin turning once again after an unfortunate accident. Rika suddenly finds herself in a "perfect" world, the constant cycle of brutal killings having never taken place, where all of her friends are content and satisfied. Not wanting to abandon the world that she fought so hard for, she learns she must destroy an essential "key" to get back. But can Rika abandon the faultless world she is given the chance to live in, after all of her battles have brought her this far?

The story is set in the year 311 of the Orbital Calendar, when humanity has migrated to countless colony clusters in space. A space colony girl named Akiha Shishidou encounters a malevolent artificial intelligence named Leopard that has been installed on a colony. Akiha is joined by an Inter-Colony Police officer named Itsuki Kannagi, a taciturn young girl named Honoka Kawai, and a robot named Imoko "Imo-chan" Shishidou.

These are a series of 13 omake episodes of Gun x Sword, tied in very loosely to the plot, with the characters as chibi puppets. The main characters are Wendy and her turtle, Kameo, who is the size of a human in this series and is able to talk. All the episodes seem to center around analyzing various events in Gun x Sword and mocking the themes displayed. They are included on the DVDs.