Here is the official story outline as posted on the Square Enix site.

Two years have passed since the fated battle. 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.

And so Cloud, who walked away from the life of a hero to live in solitude, must step forward yet again.