Perhaps Seph was using his will to manipulate Jenova's headless (and presumably insensate) body, after it was sprung from Shinra HQ?
That is my belief, and a theory I peddled at FFO quite some time ago. There are three other prevailant ideas people come up with in these debates, but I personally find them to be flawed.

-"We are following a real Sephiroth clone" - this is clearly full of holes. A perfect genetic copy of Sephiroth, and nobody ever mentions this astounding scientific breakthrough in the game? Silly.

-"We are following a projection of Sephiroth" - On the surface this is rather sound. I myself have problems believing Sephiroth can emit a corporeal mental projection of himself from the North Crater, without there ever being a mention of such an amazing ability.

-"We are following Jenova who's pretending to be Sephiroth" - Ok...but why would she do this? Why does nobody ever mention Jenova's plot to impersonate Sephiroth? Why is there just one line of dialogue from Jenova if she's such an important part the story? Why does the entire game build up Sephiroth as the main villain? You can see I don't like the idea.

Possible problems with my theory

-"The tattoo Dio mentions." - A number one tattoo. Why the hell not? Wasn't Sephiroth the first known product of the Jenova project? It's not only Sephiroth clones who get tattoos, didn't Red XIII have one?

-"Nobobdy ever comes out and says this" - Indeed, and it's a bitch, but nobody ever directly clears up this point of the story, which is why we're discussing it. Although, if you have Yuffie in your party when defeating Jenova DEATH, then afterwards she'll say "You mean we were following THAT THING this whole time?" To me, this is a killshot to both the "clone" and "projection" theories.

-"Didn't Cloud say Sephiroth was carrying Jenova with him?" - Yes, and that is slightly damning...or is it? It's my belief that Cloud saw Sephiroth, fought Jenova, then jumped to his own conclusions. This line is it an early part of the game where we're just dipping our toes in the great lake that is FFVII's story, and I don't think we should rely on Cloud's possibly confused conclusions as gospel truth.


So there. People might disagree, but I firmly believe Sephiroth manipulated Jenova's headless body when the time for the Reunion came. He bust out of the container, assumed his own human form, freed Cloud, killed many people including President Shinra, began to gather the clones and then headed off for the Black Materia and eventually the Reunion. It took a bloody long time to work out that theory, but I'm sticking with it