I think that sephiroth is in control but he has such a large concentration of the jenova cells that he wants the same thing as her to destroy all life and use earth as a ship to do the same thing in another solor system but he seems to think and act on his one because he also wants infinite power he told cloud that when meteor struck and all the life stream came to fix the wound he would be at the center and absorb it all and become a god, jenova on the other hand just wants to bring death, destruction, and caos