After trying to rescue a man on the subway tracks, two teens wake up in a room dominated by a mysterious black sphere that sends them to hunt down and kill aliens hiding on Earth.

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.

Two teenage best pals attracted to the same boy end up scrambling his life after he walks into a door and is knocked unconscious.