Quote Originally Posted by The Crystal View Post
After the Nibelheim incident, both Cloud and Zack were injected with Jenova cells. Hojo did this, because he wanted to test his theory about the Reunion. Hojo knew that the Reunion would happen, and because of this, he injected Jenova cells in the citizens of Nibelheim that survived Sephiroth's attack, to study them and the Reunion process(these people were the black cape guys/girls). Zack and Cloud were part of this experiment.
Actually, Zack already had a Jenova injection before being captured from being a soldier, which probably explains why he was largely unresponsive to the injections and mako showering.

Because of the experiments in Nibelheim. Cloud and Zack were injected with Jenova cells and Mako, and this made Zacks memories go to Cloud's mind. And because of Cloud's weak mind, and his desire to become a SOLDIER, he convinced himself that that memories were his owns, and he was a SOLDIER.
I'd always viewed it as a defense mechanism than anything else, really. He didn't mean to replace himself with Zack conciously, but since Zack had been telling him all these stories, and because Zack represented what he wanted to be, he took the image of Zack and made it his image to give himself an anchor while his real mind restored itself. It might have worked too, if not for Sephiroth's interference.

And Tifa knew that Cloud was there, because of the retconn in Last Order. But the explanation of why she didn't told Cloud during the game, is not revealed.
Actually, I don't think she remembered seeing him. Her expression in LO is slightly glazed, and given that she had just taken some serious blunt force trauma, her long term memory might be on the fritz. She does have a history of not remembering the moments just before a serious accident, such as the falling incident when she was eight.