Quote Originally Posted by SoS's FAQ
Does this mean that Sephiroth really is the Puppet Master of Final Fantasy
VII? Yes. JENOVA's instincts play out through Sephiroth, however, it was not
consciously manipulating or controlling him into doing anything, nor was he
technically controlling it. He WAS JENOVA, or, rather, it's evolved form.
There was not any puppeteering going on except that which was exerted over
Cloud and the black-cloaked Clones from Nibelheim. There was just growth.
Sephiroth could control all of JENOVA's Cells that were disembodied and could
manipulate those in whom they were injected, but he was not controlling JENOVA
because the JENOVA that the Cetra had known no longer existed and all that
remained was him. He simply grew as a mutation of JENOVA.
i believe this clears up who was the puppet master.