There are a few major conflicts that need to be resolved within the game's story.
a)The war between Mechea and the Empire, and their creation of The Synthetic Unkindness.
b)Defeating The Lunatic and stopping him from destroying existence.
c)Defeating The Puppet Master and preventing him from becoming a god.
d)Reincarnating the planet while destroying The Harbinger.
These are the four major conflicts that will be resolved throughout the story. The first quarter of the game revolves around the resolution of the eight character arcs and their coming together. The second and third involve the discovery of the truth behind the war, taking down the two super powers, and Vance's discovery of what he is. The last quarter of the game involves defeating both The Lunatic and The Puppet Master.