Jenova is dead, Sephiroth is dead, and Meteor has been stopped. Now, the inhabitants of the Planet are slowly rebuilding, though with much anguish and despair. The disease known as Geostigma that appeared after the Lifestream receded currently plagues them. They had no idea that the events of Meteor have brought a being to Gaia that can only compound the suffering...

The cosmic being called the Sentience Of The Universe intervenes in the affairs of the worlds to prevent an impending cosmic destruction brought on by the actions of Organization XIII, who have mistakenly disturbed the balance between Light and Darkness.