the l'Cie becomes evil essentially, turning their Focus into a mindless "dark servant" (translated from japanese text). you spend the last 2 dungeons without the ability to use magic OR summons, it's basically a really long on-rails shooting scene. It's a big "technology vs magic" showdown, and every the fal'Cie is banished in the end, but the explosion rocks Cocoon. Lightning is herself a fal'Cie and she disappears in the end.

juz kidding,spoiler made up only.