Mass of Complexes
Most people who've spent any amount of time thinking about Final Fantasy 7 will agree that Sephiroth is not the ultimate villain of the game. True, he is the final boss, but he is not the motivating force behind the evil afoot. Rather, most people come to the conclusion that either Jenova or Hojo bears most of the blame for the suffering of the main characters. Whether they focus on Hojo or Jenova depends on how they interpret the vague hints given through the game. However, these characters are more alike than most people realize.
In her only line of the game, Jenova calls Cloud a puppet. The implication is that she is the puppeteer, not only of him, but of Sephiroth, the clones, and the plot of FF7 itself. To what degree she was puppeting Hojo is left to the imagination.
It is generally asserted that Hojo's work with the Jenova Project came between him and Lucrecia. This could have occured in several ways. The simplest explaination is that Hojo is simply an obsessive workaholic willing to sacrifice both his marriage and his son to the Project. While a valid explaination, I don't think this really fits the tone of the game and the backstory. Hojo and Lucrecia clearly kiss, and it's assumed that they loved each other at one point.
So was Hojo merely Jenova's puppet thoughout the game? I don't think it's that simple either. Jenova would have had to be puppeting Hojo long before he had any opportunity to inject himself with her cells. That's just not likely. If Jenova could puppet the people in the lab, surely she'd have a more direct way of getting out of that formaldehyde chamber than the 25 years it took just to get her head free.
And yet... Seemingly out of nowhere, Hojo clutches his head and writhes in pain before shooting Vincent in the flashback. What other character in the game is known for clutching his head and writhing in pain? Cloud. Specifically, Cloud when Jenova or Sephiroth are speaking into his head. Suppose Jenova was not puppeting Hojo, but speaking to him?
Why Hojo, instead of Lucrecia or Gast? Sephiroth describes Hojo as a "mass of complexes". While these complexes could be due to later events, I think it's likely that Hojo was already somewhat unstable before the Project began. After all, most people hearing a voice in their head would brush it off. Hojo accepted it. Hojo and Jenova likely drove each other further insane as time passed. After all, wouldn't you go mad if you were being held in a formaldehyde chamber and could only talk to one unstable scientist who might or might not do as you asked? And wouldn't you go mad if you lost your wife to this Project you'd staked both your reputations on, and you knew you'd let her die because you were too busy listening to the voice in your head?
Neither Hojo nor Jenova cared who had to get hurt, they only knew that they could each use the other to get what they wanted. Perhaps in some way, they even loved each other. After all, Hojo dedicated his life to Jenova, and he was the only one she could talk to for many years. In a game full of unrequited romances, wouldn't that be appropriate?