Based on the real life events around Yevfimy Vasilyevich Putyatin, a Russian admiral noted for his diplomatic missions to Japan and China, and the signing of the Treaty of Shimoda in 1855.

Less than a year after Geist activated the Death Force, which decimated most of Jerra's population, he has kept himself busy by dismantling the Death Force machines one by one. Most of the remaining human population have fled to a remote haven run by a warlord named Krauser. Krauser is another MDS unit, MD-01, who has a technology that hides his mobile fortress from the Death Force.

The film revolves around a mysterious girl named Éclair who appears before Fairy Tail, the world's most notorious wizard's guild. She lost all of her memories, except for the imperative that she must deliver two Phoenix Stones somewhere. The stones may spell the collapse of the magical world, and Natsu, Lucy, and the rest of the Fairy Tail guild are caught up in the intrigue.

The story takes place in the year 2034, two years after the events in Ghost in the Shell: S.A.C. 2nd GIG. Female cyborg Major Motoko Kusanagi has left Public Security Section 9, an elite counter-terrorist and anti-crime unit specializing in cyber-warfare, which has expanded to a team of 20 field operatives with Togusa acting as the field lead.