Jenova's goal was the Reunion, and Sephiroth's goal was to manipulate the clones by projecting his will and commanding them at great distance. These two goals worked in unison. As a 'clone' - and one with a particularly severe loss of self-identity - Cloud was useful to both of these objectives.

Jenova's headless body escaped from the Shinra building, but Sephiroth's projected will was consciously controlling matters.