*dropkicks brain*
We all know the basics. Cloud was an attempt to become a Sephiroth clone, Zack broke him out and ran, yadda, yadda, yadda.
Bunny time. I blame a doujin page.
What if Zack wakes up one day, and finds Cloud awake. Awake and a little...non-Cloud like. He's up, he's moving, and he's almost Cloud, but there are things that remind him of Seph.
And the reason that he sees those things is because Sephiroth decided to just go ahead and move into Cloud's head. Kid is a little young, but he is alive, free of Hojo's control, and with Zack. Three good reasons to take over.
So you have Cloud who's awake, kinda, and when he fades out, Sephiroth takes over fully, trying to act as Cloud-like as he can, so not to make Zack suspicious. He plans on slowly taking over fully, as he's got to get used to having a body again, and at the same time getting Zack used to the "new" Cloud.
Strange little bunny.