Jenova was told of as this insidious plague at a source that could overtake people and wear their faces to get close to others and spread her terror and influence.
People take Hojo's word as the lead expert on the Jenova project, but he's actually wrong on a few key points. He says that this is all Sephiroth and that the Reunion at the North Crater went against his initial guess of it happening at Shinra HQ where Jenova's body was stored. Everyone just assumes it's all Sephiroth leading the force, and pushing for his plan of godhood.
I disagree.
Let's actually break down what happens to Sephiroth. We see in Crisis Core that he actually had a relatively stable moral center and was disillusioned with Shinra and his upbringing. He even said he may abandon Shinra if things kept going the way they did. There was a sliver of hope for him to actually become the hero that everyone saw him as.
Then the Nibelheim incident occurred. But what happened there exactly? We see Sephiroth come to the realization that he was created similarly to the monsters being developed there, and then delves into the Jenova Project notes. Gast erroneously thought of Jenova as a Cetra, so Sephiroth believed himself to be one as well. The Cetra were the original stewards and protectors of the planet, so Sephiroth would believe that to be his birthright, not the role of humans.
But wait, doesn't that go against what else we know about the Cetra?
The Cetra were in deep communion with the Planet and could feel its pain and its needs, enough to respond to threats and protect it. Sephiroth even admits to such, that the Cetra can communicate and sense when beings returned to the planet. But learning this doesn't give him that ability. He never feels that connection. Not truly. So is he just misled? Believing some incorrect information?
If that were the case, why go through so much destruction to see Jenova? Why go through with the plan to call Meteor? Why manipulate people so thoroughly to achieve these goals, especially when Sephiroth was NEVER like that before? What changed?
Simple.
He wants to be with Jenova.
Sephiroth spent days researching and learning all about Jenova and the project, while being physically closer to her than any other SOLDIER at the time aside from Zack. Sephiroth was also uniquely created with an even greater amount of Jenova cells and grew up with them, so his connection is even stronger. Being so close and being so connected, Jenova did what she does best.
She got into his head.
Days of poring over pages and getting fed half-truths and inaccuracies, but with a purpose. He needed his own revelation as to what he was, and Jenova provided the answers he wanted. And once the thoughts were planted, Sephiroth immediately lost every other thought except to see Jenova.
The horrific experiments creating monsters?
Irrelevant. Go see Mother.
The wellbeing of his friend and comrade Zack?
Irrelevant. Go see Mother.
The lives of all those innocent people?
Irrelevant. Go see Mother.
That's not Sephiroth's thoughts.
That's The Reunion taking effect on him.
Even if Sephiroth just learned that his life was a lie, he has no reason to just attack people to openly.
But Jenova DOES. Jenova spreads fear and chaos, and now she has the most terrifying face to wear as she works her schemes.
Sephiroth takes Jenova's head and falls into the Lifestream, but we never see the head again. That's because it melded with Sephiroth so Jenova could take over, use his power to cause more Calamity, and grow ever stronger to continue her assault on the cosmos.
The Reunion at the Northern Creater wasn't focusing on Sephiroth. It was focusing on Jenova's head, which has merged INTO Sephiroth.
Oh and would you look at the Jenova fight in Revelation?
Barret asked the right question all the way back in 1997:
