Personally, I think that Sephiroth was more or less acting as the embodiment of JENOVA's will. In other words, what became his objective had been JENOVA's and was a plot more or less conceived by JENOVA, but carried out through Sephiroth, who was also conscious and acting, but based on a plot devised by JENOVA and given to him.

Certain things simply had to have been Sephiroth conscious and taking action, most notably all the work put into torturing Cloud. JENOVA would have had no reason to torture him so. Sephiroth's pride being hurt by Cloud when he beat him gave him plenty of reason to torture Cloud.

Cloud was being called to the Reunion the same as the other Sephiroth Clones, but getting him to follow hardly required rendering mental torment upon him. All that would have been necessary would be overriding his will completely and dragging him there, or showing him the image of Sephiroth on the horizon every once in a while. The entity tormenting him, however, obviously wanted him to suffer.

I believe Sephiroth continued to remain an independent entity until he and JENOVA merged at the end of the game (the process beginning in the Bizarro Sephiroth battle, in which we can see the two merging) and at that point, I feel that JENOVA's consciousness was taking over altogether, which would explain why the Sephiroth we see there said nothing, whereas the Sephiroth forms seen earlier wouldn't shut up.


Anyway, here's some thorough explanations of my views and why I hold them:

http://www.geocities.com/ff7analysis/control.html
http://www.geocities.com/ff7analysis/Symbolism.html