Was Zack a Sephiroth clone?
Originally, yes, Zack was a Sephiroth clone. All members of SOLDIER were essentially Sephiroth clones. The one and only thing that made Sephiroth special was the Jenova cells in him. The biggest difference between himself and the rest of SOLDIER was that he was born with Jenova.
SOLDIER was probably not always experimented on. SOLDIER may have at one time been the elite fighting group they are commonly thought of. But at this point, SOLDIERs have all been injected with Mako (which they know about) and with Jenova (which they possibly don’t know about).
I think the cloning project started longer ago than at Sephiroth’s death. When Sephiroth proved to be an incredible fighter, I think that’s when SOLDIERs began getting injected not only with Mako, but with Jenova cells as well to see if they could create another Sephiroth. SOLDIERs were the original clones, but Cloud and Zack and the rest of the people who managed to survive Sephiroth’s insane rage in Nibelheim became Hojo’s first actual toys. He couldn’t actually mess with SOLDIERs without looking like he was actually doing something.
Originally, Zack was a Sephiroth clone because SOLDIER was made up of Sephiroth clones. This would also explain why Cloud seemed to react to Jenova so much better than Zack did and still be called a failure. Zack already had Jenova in him, so of course he wasn’t going to react to it anymore than he already had. Cloud reacted because he’d never been subjected to them before. Cloud wasn’t mentally strong enough to deal with it, though, which is why he was later considered a failure.
So why didn’t Zack go all wonky like the rest of the clones? That’s simple. Jenova didn’t call the spread out pieces of herself until after the start of the game. The clones didn’t go wonky until after Jenova started messing with them.
Once Hojo determined that Zack wasn’t as receptive to Jenova as Cloud was, though, what happened to Zack? Well, we can’t be sure, really. Hojo had done some other sort of experimentation in the past. Look at Vincent, for example. Those monsters weren’t there before Hojo started messing with him, I don’t think. Hojo may have done something completely different to Zack.
Would Zack have come to the reunion if he had survived? Probably. Maybe he was like Cloud. Cloud acted perfectly sane, when Jenova was stringing him along. Cloud managed to do everything Jenova wanted him to without realizing it. She could have done the same thing to Zack. Zack acted perfectly sane after their escape, he may have been moving just as she wanted him to.
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