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.

Led by a strange dream, scientist Aki Ross struggles to collect the eight spirits in the hope of creating a force powerful enough to protect the planet. With the aid of the Deep Eyes Squadron and her mentor, Dr. Sid, Aki must save the Earth from its darkest hate and unleash the spirits within.