Originally posted by Raistlin
This theory's main support, IMO, comes in the North Crater early in disc 2. You see "Sephiroth" killing a bunch of clones. However, Jenova was calling the clones to the Crater to get her cells back. So what if what you were seeing was actually Jenova taking her cells back from the clones, and Cloud's just seeing what Jenova wants him to? Also, as Berrik mentioned, those Jenova battles you have after talking to Sephiroth.
One more thing: In Shinra HQ, disc 1, you follow Sephiroth on his trail of blood. Also, you see that Jenova has escaped her confinement, so she could have escaped herself and went on that killing spree. Jenova would also want revenge against Shinra, probably even more than Sephiroth himself.