I certainly did not understand where he came from and to be honest I couldn't care less. The plot was boring me. When the game gets technical and starts introducing terms like 'genome' or 'crystal' I tend to lose interest and begin hammering the X button to get to the point where I can begin playing the game again.
Having said that my theory is he just came out of nowhere after the Kuja fight. I don't know, Kuja may have summoned him after casting ultima?