Jenova:

Contrary to what Sephiroth thinks, Jenova isn't really his mother. The information he found out must have been missing a few important points, maybe nobody recorded it? Maybe Sephiroth misread/misunderstood the information? MAYBE THE BOOKS WERE LIES! (Or perhaps Sephiroth couldn't read very well! Okay, bad joke...). Because really Sephiroth is a normal human, just a bit altered +B. He was the child of Lucrecia and Hojo the two assistant scientists in the Jenova Project. When Lucrecia was pregnant Hojo decided he would inject her with Jenova cells so that she would give birth to a child with powers of the Cetra. Lucrecia agreed but after giving birth to Sephiroth she collapsed and disappeared. After thinking it through, my view is that Lucrecia did die but not a whole death, because she says in the waterfall that the Jenova cells in her won't let her die, in my view I think she means that the Jenova cells keep her soul alive and won't let her pass on peacefully.
Ah ha, but there's more, so Sephiroth thinks that Jenova is his mother but really she isn't, he also believes she is one of the Ancients, but she isn't. During the Jenova Project the last survivor of the real Cetra was found alive and well, this woman (Ifalna) was interveiwed by professor Gast, and he was told the truth about the Ancients and Jenova. The crisis which struck the planet was Jenova, who arrived on a meteor (quite possibly THE Meteor). Jenova, being the planet-hopping virus that she is then infected the Cetra who came to get rid of her, thus, wiping almost all of them out.
More on Jenova. Now you see, she had quite a big role. This particular theory I'm referring to is one that I myself believe could be very true. There is no doubt that Jenova played a big part as a villain, either she was controlling Sephiroth like Sephiroth was able to control Cloud at points for example. Or Sephiroth willingly let Jenova act through him as he believed that she was his mother. Whichever is the case, this was probably very easy for Jenova as Sephiroth was the ideal candidate as he was the first in the Jenova project and most likely had the largest percentage of Jenova cells inside him.






The Reunion:

You will hear Sephiroth mention 'the reunion' a few times in the game. So, what is the reunion? Well, mad scientist Hojo who was working on the Jenova project thought up this reunion theory, it was that if Jenova's cells were scattered they would find each other again and become one, the place where they would meet would be the promised land. It was called the reunion for the obvious reason that the cells would reunite with each other. Hojo injected test subjects with Jenova cells to see if his theory would work. These test subjects are the black-cloaked figures you see at certain places (temple of the ancients, Nibelheim, and the northern crater). They could be related to the Sephiroth copies which he controls because some of them manage to mention Sephiroth it's as if they are 'his followers'.




Something which I thought of whilst playing the game was that the citizens of Nibelheim who were killed when Sephiroth burned it down were taken away and injected with Jenova cells and turned into the black-cloacked figures that you see when you go there, I also read an agreeing theory at 'Sephiroth no Oukoku' a long time ago, so it might be right ^^;