Pyreflies. Everything in Spira happens via pyreflies. (no seriously....)

At that point, Chappu is nothing more than a bunch of pyreflies. You see pyreflies show visions of the past in the game, you know that pyreflies make spheres. Pyreflies do a lot of stuff, and the pyreflies that were once Chappu probably did it (even though you don't actually "see" any pyreflies doing anything).