Ah, Dune...I fucking love that film. I'd suggest reading the books, even though that will probably make you hate the film and question what the fuck David Lynch was on when making it. But, his version is easier to make sense of with the surrounding backstory of the books.
Basically, prophecy says that one day a male Benne Gesserit will be born and that he'll be able to see all futures and then lead the galaxy down the path to the most beneficial future (with the Benne Gesserits in control). Although the Benne Gesserits can see some futures, their arrogance leads them to believe they can manipulate the prophecy as they see fit, intending for Jessica to have only daughters so that one of the daughters can marry a Harkonen and then their son will become the Kwisatz Haderach of prophecy, uniting house Harkonen & house Atreides. However, Jessica falls in love with Leto Atreides and gives him a son, Paul, or Maud'dib as he'd later be known. Once the Benne Gesserits realise, they try and manipulate Paul, but once they realise he is beyond their control they then scheme to eliminate him, only to discover that it's already too late and Paul has realised his destiny as the Kwisatz Haderach.