Two years have passed since the final battle with Sephiroth. Though Midgar, city of mako, city of prosperity, has been reduced to ruins, its people slowly but steadily walk the road to reconstruction. However, a mysterious illness called Geostigma torments them. With no cure in sight, it brings death to the afflicted, one after another, robbing the people of their fledgling hope.

The film’s story begins when Arata inadvertently touches “Hermes Apocrypha,” Lilith’s Grimoire. Suddenly, he is enveloped by a bright white light, and a girl appears before him. She calls herself Lilim, and treats both Arata and Lilith as her parents. At the same time she appears, something changes in the world. The forbidden Eternal Library awakens. In the Library is sealed the ultimate culmination of Alchemy, the White Demon Lord. The White Demon Lord plots to eliminate Arata and the Trinity Seven to usurp the position of Demon Lord. Bristling with untold power, the White Demon Lord attacks Arata, and triggers a desperate crisis where Arata and the Trinity Seven must save the world in this last battle.

Akiko, a young woman, comes to Vladivostok to meet Matsunaga, a young businessman she has met in Tokyo only once. Akiko finally finds Matsunaga. However, he leaves her again, warning her not to trust strangers in a foreign country. She tries to follow him, but she is attacked by thugs and dumped on the outskirts of town.