I couldn't link to the theory to see if this guys theory is similiar to what I'm going to say so sorry if I'm repeating anything...
I don't remember the game ever giving him any motive outside of his speech when he first appears but I could have sworn he's basically hinted to at the villiage of the Summoners (forgive me, it's been ages since I played this game) If you read the writing on the wall, they tell a story about the summoners using the great crystal to summon in their experiments, and they brought forth a terrible evil that threated to destroy the world. They ended up using the great crystal to seal him within it, and they broke the crystal into four pieces so there would be no chance of his return.
That's why I thought Necron appears at the end cause Kuja restored the crystal and then destroyed it after he was defeated. I could be wrong though:rolleyes2