The story is that the world's gonna end in 13 days, and Bhunivelze has tasked Lightning with saving humanity from the chaos and bringing them to the new world that will be created. Noel's fighting Lightning out of shock, refusing to believe it truly is her.
Considering that Bhunivelze's utterly matricidal and Lightning's at odds with herself "directing the destruction of the world", I wouldn't be surprised if the god of light is the main antagonist. And yeah, it takes place 500 years after XIII-2 on the remains of Gran Pulse, where people can neither age nor bear children.
"The only thing that gets me high is the musky scent of my enemy's fear.'' - Stephen Colbert http://s1136.photobucket.com/albums/n496/Elice_Carol/