FF7

[James]

Cloud left Nibelheim to join SOLDIER. He didn't make it, but Zack did. Then they had a mission in Nibelheim, where Zack and Cloud joined Sephiroth. Sephiroth learned of his origins, and went nuts. Cloud killed Sephiroth, and his body fell into the lifestream (and settled in the North Crater).

Meanwhile, Cloud and Zack were "apprehended" and infused with Jenova. Cloud ended up getting all messed up from it, but Zack was not (possibly due to the Mako exposure). They escaped, only to have Zack killed, and Cloud left for dead. He took Zack's sword, and crawled to Midgar.

His own shame and his fucked up state caused him to take on part of Zack's life in his own mind. He made himself believe he was in Soldier the whole time. He put himself in Zack's place.

So Tifa never knew Cloud actually was at Nibelheim, but she knew Zack was. She knew Cloud put himself in Zack's place for some reason, and she thought that maybe this Cloud was a clone or something. She didn't really know what to say or how to say it, so she just didn't say anything.

Jenova wasn't an Ancient. He/She/It was just a destructive force.