I have no idea why Lynch would put in that rain scene. It's like he paid no attention to anything mentioned about sandworms - water kills them. So making it rain would have killed every sandworm in the vicinity of Arrakeen.
If I remember right, either producer Dino de Laurentiis, Universal CEO Sid Sheinberg or both forced that ending on Lynch. Lynch's original scripted ending was consistent with the novel; however, they wanted a more triumphant note to end the film on than 'Paul becomes Emperor, has a loveless marriage with Irulan, ignites a universe-wide jihad that kills tens of billions of innocent people'.
"C'mon, this is Hollywood!! This guy's supposed to be a Messiah, right? Let's see a miracle!"
PAUL: We Fremen have a saying: "God created Arrakis to test the faithful." (staring hard at the Reverend Mother) One cannot go against the word of God.
REVEREND MOTHER: (in horror) You speak of Holy War... You bring the Jihad!!
PAUL: Yes. The human race feels the need for the cleansing turmoil - a holy war that will rage across the universe. Genes will mingle, and strong new mixtures will survive. I did not want this. I have long resisted it. But you, like spoiled children, insisted on it. And it. Will. Be.
(The Fedaykin begin beating their drums again)
REVEREND MOTHER: You cannot unleash these people on the Universe!!!
PAUL: (torturing her with the Voice) You will yearn for the gentle ways of the Sardukar. I have already seen the destruction you have sent falling down around your heads. I accept this treachery. I accept my place in it, though I am not the cause. Now, I lead you on the burning path to the new world!
ALIA: And how can this be? For he IS the Kwizatz Haderach!!
(We zoom in through Paul's blue eyes to see a roaring ocean. As we watch, a gigantic wind rises up - and the ocean turns blood red. ROLL CREDITS.)
REVEREND MOTHER: (in horror) You speak of Holy War... You bring the Jihad!!
PAUL: Yes. The human race feels the need for the cleansing turmoil - a holy war that will rage across the universe. Genes will mingle, and strong new mixtures will survive. I did not want this. I have long resisted it. But you, like spoiled children, insisted on it. And it. Will. Be.
(The Fedaykin begin beating their drums again)
REVEREND MOTHER: You cannot unleash these people on the Universe!!!
PAUL: (torturing her with the Voice) You will yearn for the gentle ways of the Sardukar. I have already seen the destruction you have sent falling down around your heads. I accept this treachery. I accept my place in it, though I am not the cause. Now, I lead you on the burning path to the new world!
ALIA: And how can this be? For he IS the Kwizatz Haderach!!
(We zoom in through Paul's blue eyes to see a roaring ocean. As we watch, a gigantic wind rises up - and the ocean turns blood red. ROLL CREDITS.)
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