Perhaps one of the most intersting questions left unanswered in Dune is what exactly the Bene Gesserit wanted with the Kwisatz Haderach. Yes, we know they had their generations long breeding program to create the Kwisatz Haderach, their super-mentat, but what did they want to do with him when he finally arrived? This is a question that we discussed in class but never obtained a satisfactory answer to. Jeesh adresses the same question in one of his previous posts. He maintains that the Bene Gesserit suffered from goal displacement. That they in fact no longer knew what they wanted to do with the Kwisatz Haderach, but only knew that they were trying to create him. Although this is certainly a logical answer to the question it is not one that I agree with. I say this because as Dune is taking place the Bene Gesserit were very close to creating the Kwisatz Haderach. In fact they expected he might come from the union of Feyd-Rautha Harkonnen and the daughter that Jessica was supposed to have. Paul was really only one generation off. This means that as Dune is taking place the Bene Gesserit must have been thinking about what to do with Kwisatz Haderach for some time now as they drew ever closer to their goal. What this means is that even if Jeesh is right and they suffered from goal displacement then they would have come up with a new use for the Kwisatz Haderach in the years prior to Paul's birth.
I think one possibility is that the Bene Gesserit hoped to use the Kwisatz Haderach to furhter their own political goals. That they wanted to use him to gain even more power in the power structure of the empire. After all, as Paul surmised very early in the book the Bene Gesserit is all about politics (that is what he told the Reverend Mother before she tested him with the gom jabbar). It is true that the Bene Gesserit seem to have an immense ammount of political power as it is, but with the Kwisatz Haderach, one who is essentially a super-mentat with prescient abilities, behind them they could gain so much more power. In fact with such a person behind them perhaps the Bene Gesserit hoped to move out of the shadows and take power openly.
Another possibility is that after the carnage of the Butlerian jihad the Bene Gesserit took it upon themselves to make sure that the very best traits of humanity were preserved and passed down. Perhaps their breeding program was merely their way of improving the human species. This would explain their desire to seperate humans from "animals" through such testing as the gom jabbar. I think it is possible that the search for the Kwisatz Haderach was actually a secondary goal that developed later in the Bene Gesserit program. This might explain why they did not seem to have a clearly defined plan on what to do with the Kwisatz Haderach.

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