No, Jenova was a tool. While she was responsible for the destruction of the Cetra, she was technically killed by the remaining ones and her body used as a tool by Shinra and specifically Hojo when they found it. While Sephiroth claims what he's doing is his "mother's" will, it's really more like he came to his own conclusions after reading everything he could find in the underground library in Nibelheim and decided that the desires and goals he felt to complete were the same as what Jenova wanted, not that he himself honestly knew or was being told what they were. On top of that, Jenova was already brain dead by this point as Ryushikazu has already pointed out; she had absolutely no control over what was going on, and was merely a tool. A tool, therefore, cannot be described as the villain of the game.Originally Posted by Odd Eye
That being said, I agree that Sephiroth is the antagonist in the game, but not the main villain. I personally found Hojo to be, both directly and indirectly. Much of what occurs happens because of Hojo (the use of Jenova cells, the creation of Sephiroth, the acknowledgment of Aeris by the Shinra corporation, ect.), though it could be debated whether or not all of this was purposely planned by Hojo or merely a lucky result due to his own ineptitude and desire for power. So while Sephiroth is the major threat, we could consider Hojo to be the actual villain in this story do to the fact that so many of the problems stem from his involvment.
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